Variant report

Variant	rs2330593
Chromosome Location	chr21:47932808-47932809
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1023355	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11910493	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17393980	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2096507	0.83[YRI][hapmap]
rs2839260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2839282	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2839291	0.82[ASN][1000 genomes]
rs2839293	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2839300	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2839323	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2839324	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2839338	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2839340	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2839361	1.00[JPT][hapmap]
rs2839362	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2839366	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4312581	0.91[ASN][1000 genomes]
rs4818844	0.82[ASN][1000 genomes]
rs4818845	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4819258	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4819259	0.82[ASN][1000 genomes]
rs4819260	0.82[ASN][1000 genomes]
rs4819261	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs55735202	0.82[ASN][1000 genomes]
rs55992430	0.82[ASN][1000 genomes]
rs60522135	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6518296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs66514870	0.82[ASN][1000 genomes]
rs66596180	0.82[ASN][1000 genomes]
rs66991124	0.82[ASN][1000 genomes]
rs67285811	0.82[ASN][1000 genomes]
rs7276841	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs743347	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7510435	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8131943	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9977528	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9981156	0.82[ASN][1000 genomes]
rs9981272	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9981276	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9982358	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9984082	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9984590	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	nsv1058397	chr21:47851176-48091343	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
19	nsv459312	chr21:47856106-47985655	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
20	nsv587998	chr21:47856106-47985655	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers 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
21	nsv1065502	chr21:47865215-48091343	Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
22	nsv1056152	chr21:47875370-47979259	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers 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
23	nsv1061442	chr21:47875370-48091343	Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
24	nsv1059466	chr21:47894705-48096945	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	n/a
25	nsv1061185	chr21:47901250-48096945	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	n/a
26	nsv1057566	chr21:47915583-48029698	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2330593	SPATC1L	cis	Whole Blood	GTEx
rs2330593	SPATC1L	cis	Thyroid	GTEx
rs2330593	SPATC1L	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47911400-47933600	Strong transcription	Fetal Muscle Trunk	muscle
2	chr21:47913000-47935000	Weak transcription	Right Atrium	heart
3	chr21:47915200-47933400	Strong transcription	Fetal Stomach	stomach
4	chr21:47919400-47933400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr21:47920600-47935600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr21:47921400-47933400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr21:47921800-47933000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr21:47923000-47933000	Strong transcription	Fetal Intestine Large	intestine
9	chr21:47924000-47933400	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr21:47924000-47933800	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr21:47924200-47933600	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr21:47924200-47933600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr21:47924200-47933800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr21:47924400-47933000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr21:47925600-47933800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr21:47927400-47950000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr21:47927600-47933000	Strong transcription	Fetal Muscle Leg	muscle
18	chr21:47927800-47933400	Strong transcription	Fetal Lung	lung
19	chr21:47928000-47933000	Strong transcription	Left Ventricle	heart
20	chr21:47928000-47933600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr21:47928200-47933400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr21:47928400-47933000	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr21:47928400-47933000	Strong transcription	Fetal Thymus	thymus
24	chr21:47928400-47933800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr21:47928600-47933000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr21:47928600-47933000	Strong transcription	Fetal Brain Female	brain
27	chr21:47928600-47933400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr21:47928600-47933600	Strong transcription	NHEK	skin
29	chr21:47928800-47933000	Strong transcription	HUVEC	blood vessel
30	chr21:47928800-47933400	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr21:47928800-47933400	Strong transcription	Primary hematopoietic stem cells	blood
32	chr21:47928800-47933800	Strong transcription	Brain Germinal Matrix	brain
33	chr21:47928800-47936000	Strong transcription	Placenta	Placenta
34	chr21:47929000-47933000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr21:47929000-47933000	Strong transcription	Adipose Nuclei	Adipose
36	chr21:47929000-47933000	Strong transcription	Liver	Liver
37	chr21:47929000-47933000	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr21:47929000-47933000	Strong transcription	Stomach Smooth Muscle	stomach
39	chr21:47929000-47933200	Strong transcription	Primary B cells from cord blood	blood
40	chr21:47929000-47933200	Strong transcription	Brain Substantia Nigra	brain
41	chr21:47929000-47933400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr21:47929000-47933400	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr21:47929000-47933400	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr21:47929000-47933600	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr21:47929000-47933600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr21:47929000-47933600	Strong transcription	Brain Anterior Caudate	brain
47	chr21:47929000-47933800	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr21:47929000-47934000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr21:47929000-47934000	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr21:47929000-47934000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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