Variant report

Variant	rs2839252
Chromosome Location	chr21:47843923-47843924
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr21:47843775-47843937	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr21:47843826-47844487	K562	blood:	n/a	n/a
3	ZNF263	chr21:47843756-47844218	HEK293-T-REx	kidney:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:47842082..47844141-chr21:47845967..47848443,2	K562	blood:
2	chr21:47838816..47841237-chr21:47842476..47844122,2	K562	blood:
3	chr21:47841259..47843546-chr21:47843811..47847040,4	K562	blood:
4	chr21:47841235..47843966-chr21:47874444..47876872,2	K562	blood:
5	chr21:47843264..47847636-chr21:47874814..47878644,6	K562	blood:
6	chr21:47843582..47848242-chr21:47854131..47857783,6	K562	blood:

No data

Variant related genes	Relation type
RPL18AP2	TF binding region
ENSG00000225043	Chromatin interaction
ENSG00000160299	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10470249	1.00[ASN][1000 genomes]
rs11508685	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1556338	1.00[ASN][1000 genomes]
rs16979254	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892693	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs2839165	1.00[CEU][hapmap]
rs2839195	0.87[CEU][hapmap]
rs2839219	1.00[ASN][1000 genomes]
rs2839260	0.94[YRI][hapmap];0.83[AFR][1000 genomes]
rs2839264	1.00[ASN][1000 genomes]
rs2839266	1.00[ASN][1000 genomes]
rs2839303	1.00[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839315	1.00[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839316	1.00[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4365550	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs4438580	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs55808731	1.00[ASN][1000 genomes]
rs55878170	1.00[ASN][1000 genomes]
rs56034615	1.00[ASN][1000 genomes]
rs56083834	1.00[ASN][1000 genomes]
rs7283507	1.00[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73144798	1.00[ASN][1000 genomes]
rs73146707	1.00[ASN][1000 genomes]
rs73146709	1.00[ASN][1000 genomes]
rs73146739	1.00[ASN][1000 genomes]
rs73148704	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73152856	1.00[ASN][1000 genomes]
rs73152858	0.81[EUR][1000 genomes]
rs747439	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs8133508	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:36 , 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	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	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
30	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
31	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
32	nsv1056321	chr21:47835146-47973412	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
33	nsv515801	chr21:47836122-47863025	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
34	nsv819608	chr21:47836122-47863025	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
35	nsv917208	chr21:47836346-47988603	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
36	nsv914146	chr21:47838123-47858248	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2839252	SPATC1L	cis	Whole Blood	GTEx
rs2839252	FTCD	cis	Thyroid	GTEx
rs2839252	SPATC1L	cis	Thyroid	GTEx
rs2839252	C21orf57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 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	chr21:47803200-47872400	Weak transcription	Fetal Kidney	kidney
3	chr21:47814400-47861000	Weak transcription	Fetal Brain Male	brain
4	chr21:47818400-47850200	Weak transcription	Small Intestine	intestine
5	chr21:47820400-47851200	Weak transcription	NH-A	brain
6	chr21:47823200-47850200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr21:47827400-47866600	Strong transcription	Fetal Stomach	stomach
8	chr21:47828000-47863200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr21:47828600-47872400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr21:47829400-47862600	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr21:47829400-47867800	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr21:47829600-47862800	Strong transcription	Skeletal Muscle Male	skeletal muscle
13	chr21:47829600-47864000	Strong transcription	Fetal Intestine Small	intestine
14	chr21:47830200-47862800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr21:47830400-47862800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr21:47831000-47857600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr21:47832800-47847000	Weak transcription	Fetal Lung	lung
18	chr21:47833400-47863400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr21:47834000-47868200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr21:47834200-47868200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr21:47836800-47872400	Weak transcription	Right Atrium	heart
22	chr21:47837200-47847000	Weak transcription	NHDF-Ad	bronchial
23	chr21:47837800-47854800	Weak transcription	K562	blood
24	chr21:47838000-47845600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr21:47838000-47853600	Strong transcription	Lung	lung
26	chr21:47838400-47849800	Weak transcription	Osteobl	bone
27	chr21:47838400-47852200	Strong transcription	NHLF	lung
28	chr21:47838600-47847400	Weak transcription	HUVEC	blood vessel
29	chr21:47838800-47844000	Weak transcription	Aorta	Aorta
30	chr21:47838800-47846800	Weak transcription	HMEC	breast
31	chr21:47838800-47862800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr21:47839600-47845800	Weak transcription	Brain Substantia Nigra	brain
33	chr21:47840000-47847600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr21:47840000-47850200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr21:47841000-47847200	Weak transcription	Hela-S3	cervix
36	chr21:47841000-47847400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr21:47841200-47849800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr21:47841200-47852400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr21:47841400-47848600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr21:47841600-47845400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr21:47841800-47844000	Enhancers	Primary T cells fromperipheralblood	blood
42	chr21:47842000-47847800	Genic enhancers	Fetal Thymus	thymus
43	chr21:47842200-47850200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr21:47842400-47844000	Weak transcription	Gastric	stomach
45	chr21:47842400-47844200	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr21:47842400-47848400	Weak transcription	Psoas Muscle	Psoas
47	chr21:47842600-47844000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr21:47842600-47844200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr21:47842600-47845000	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr21:47842600-47845200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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