Variant report

Variant	rs61640854
Chromosome Location	chr21:47804556-47804557
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47801390..47803383-chr21:47804116..47807497,3	K562	blood:
2	chr21:47796873..47800064-chr21:47803863..47807599,5	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs16979162	0.87[AMR][1000 genomes]
rs2073378	0.81[AFR][1000 genomes]
rs57095035	0.87[AMR][1000 genomes]
rs57261762	0.84[AMR][1000 genomes]
rs58559714	0.87[AMR][1000 genomes]
rs59122923	0.87[AMR][1000 genomes]
rs7276882	0.87[AMR][1000 genomes]
rs73379348	0.87[AMR][1000 genomes]
rs73907473	0.82[AFR][1000 genomes]
rs73907474	0.84[AFR][1000 genomes]
rs73909504	0.87[AMR][1000 genomes]
rs73909505	0.84[AMR][1000 genomes]
rs8126647	0.84[AMR][1000 genomes]
rs8129435	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:46 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
2	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
3	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
4	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
5	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
6	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a
7	nsv470910	chr21:47353775-48084988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
8	nsv1059118	chr21:47398331-48090457	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
9	nsv544494	chr21:47398331-48090457	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
10	nsv934264	chr21:47401083-48090317	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
11	nsv1060978	chr21:47488073-47833640	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	n/a
12	nsv519904	chr21:47583506-47881309	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
13	nsv948761	chr21:47587940-48069930	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	n/a
14	nsv1055239	chr21:47591378-48090317	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
15	nsv544495	chr21:47591378-48090317	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
16	nsv933354	chr21:47609029-47851401	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	n/a
17	nsv949706	chr21:47625544-48069930	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
18	nsv529496	chr21:47634193-48090317	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
19	nsv587975	chr21:47661235-47830843	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	n/a
20	nsv432159	chr21:47673247-47854392	Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	n/a
21	nsv527355	chr21:47678774-47863025	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	n/a
22	nsv914136	chr21:47681041-47900994	Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	n/a
23	nsv914137	chr21:47700498-47862624	Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	n/a
24	nsv914138	chr21:47700498-47866227	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	n/a
25	nsv914140	chr21:47712185-47866227	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	n/a
26	nsv933061	chr21:47746204-48031515	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	n/a
27	nsv1062858	chr21:47750884-48091343	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
28	nsv914142	chr21:47772468-47866227	Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
29	nsv1062683	chr21:47788763-47851236	Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
30	nsv914143	chr21:47792874-47862624	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
31	nsv914144	chr21:47792874-47866227	Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
32	esv1006886	chr21:47799777-47804819	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
33	nsv587981	chr21:47800592-47841941	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
34	esv3503177	chr21:47800724-47805722	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
35	esv3488766	chr21:47801174-47805572	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
36	esv3455432	chr21:47801224-47806222	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
37	esv3455434	chr21:47801817-47804700	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
38	esv3455433	chr21:47801827-47804672	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
39	esv3455435	chr21:47801827-47804672	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
40	esv3488767	chr21:47801848-47804659	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
41	esv3488768	chr21:47801848-47804659	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
42	esv17943	chr21:47801944-47804584	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
43	nsv821371	chr21:47801944-47804584	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
44	esv3357669	chr21:47802374-47804872	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
45	nsv587995	chr21:47803949-47877594	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
46	nsv914145	chr21:47804438-47866227	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs61640854	SPATC1L	cis	Skin Sun Exposed Lower leg	GTEx
rs61640854	SPATC1L	cis	lung	GTEx
rs61640854	SPATC1L	cis	Thyroid	GTEx
rs61640854	SPATC1L	cis	Adipose Subcutaneous	GTEx
rs61640854	C21orf57	Cis_1M	lymphoblastoid	RTeQTL
rs61640854	SPATC1L	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47775600-47857600	Weak transcription	Stomach Mucosa	stomach
2	chr21:47787200-47813200	Weak transcription	NH-A	brain
3	chr21:47787400-47817000	Weak transcription	Small Intestine	intestine
4	chr21:47787800-47813600	Weak transcription	Colon Smooth Muscle	Colon
5	chr21:47788000-47813000	Weak transcription	NHDF-Ad	bronchial
6	chr21:47788000-47813600	Weak transcription	HUVEC	blood vessel
7	chr21:47789400-47807200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr21:47789400-47842600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr21:47789800-47804800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr21:47789800-47805600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr21:47789800-47809000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr21:47790000-47822000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr21:47790400-47805800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr21:47790600-47805800	Weak transcription	Colonic Mucosa	Colon
15	chr21:47792200-47804600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr21:47792200-47812800	Weak transcription	Fetal Brain Male	brain
17	chr21:47792400-47810200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr21:47793000-47809000	Weak transcription	Osteobl	bone
19	chr21:47795000-47804600	Weak transcription	Fetal Heart	heart
20	chr21:47795000-47806000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr21:47795000-47821200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr21:47795800-47806200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr21:47796000-47809800	Weak transcription	HSMMtube	muscle
24	chr21:47796200-47804600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr21:47796600-47805400	Weak transcription	Placenta	Placenta
26	chr21:47797200-47805800	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr21:47797200-47806000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr21:47797200-47812200	Weak transcription	Right Atrium	heart
29	chr21:47798000-47804600	Weak transcription	Right Ventricle	heart
30	chr21:47799200-47805400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr21:47799800-47804600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr21:47801200-47804800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr21:47801200-47804800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
34	chr21:47801200-47826200	Strong transcription	Fetal Stomach	stomach
35	chr21:47801400-47804800	ZNF genes & repeats	Thymus	Thymus
36	chr21:47801400-47805400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr21:47801400-47805800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
38	chr21:47801400-47825000	Strong transcription	Primary T cells from cord blood	blood
39	chr21:47801600-47804600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr21:47801600-47804800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr21:47801600-47804800	ZNF genes & repeats	GM12878-XiMat	blood
42	chr21:47801600-47805000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr21:47801600-47805200	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr21:47801600-47805400	Strong transcription	Fetal Lung	lung
45	chr21:47801600-47805800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr21:47801600-47805800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr21:47801600-47807000	Strong transcription	Primary hematopoietic stem cells	blood
48	chr21:47801600-47812000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr21:47801600-47813200	Strong transcription	Stomach Smooth Muscle	stomach
50	chr21:47801800-47804800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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