Variant report

Variant	rs2301639
Chromosome Location	chr3:50380661-50380662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:50371739..50377775-chr3:50378206..50384768,10	MCF-7	breast:
2	chr3:50359840..50362158-chr3:50378433..50381036,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068001	Chromatin interaction
ENSG00000068028	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10510755	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12629572	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs12635953	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1989839	1.00[CEU][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs2071802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2071803	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073498	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073499	0.93[CEU][hapmap]
rs2097247	0.92[ASN][1000 genomes]
rs2233474	0.93[CEU][hapmap]
rs2236939	0.86[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap]
rs2236950	1.00[ASW][hapmap];0.81[GIH][hapmap];0.94[MKK][hapmap]
rs2236967	1.00[ASW][hapmap]
rs2236968	1.00[ASW][hapmap]
rs2236988	1.00[ASW][hapmap]
rs2239801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282756	1.00[ASW][hapmap]
rs2526392	0.95[GIH][hapmap]
rs2526394	0.95[GIH][hapmap]
rs2526395	0.95[GIH][hapmap]
rs2526396	0.95[GIH][hapmap]
rs2624837	0.95[GIH][hapmap]
rs2624842	0.95[GIH][hapmap]
rs28365992	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3755832	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3806708	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs41291724	0.92[ASN][1000 genomes]
rs4141060	0.93[CEU][hapmap]
rs45536634	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57319506	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57462170	0.81[EUR][1000 genomes]
rs57838764	0.89[EUR][1000 genomes]
rs58051625	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60247651	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6776145	1.00[CEU][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs762898	1.00[ASW][hapmap]
rs7642692	0.94[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
6	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
7	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
8	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
9	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
10	nsv590254	chr3:50243510-50388607	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
11	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
12	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
13	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
14	nsv590257	chr3:50302830-50393640	Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS 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 miRNA target site	82 gene(s)	inside rSNPs	diseases
15	nsv590256	chr3:50302830-50420554	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
16	nsv876774	chr3:50302830-50436827	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
17	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
18	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
19	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
20	nsv590258	chr3:50368278-50381022	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
21	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2301639	NEK4	cis	parietal	SCAN
rs2301639	SLC25A20	cis	cerebellum	SCAN
rs2301639	TRAIP	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50378600-50383200	Weak transcription	Aorta	Aorta
2	chr3:50378600-50384800	Weak transcription	Dnd41	blood
3	chr3:50378800-50382400	Weak transcription	Brain Angular Gyrus	brain
4	chr3:50378800-50382400	Weak transcription	Pancreas	Pancrea
5	chr3:50378800-50382600	Weak transcription	HUVEC	blood vessel
6	chr3:50378800-50382800	Weak transcription	Ovary	ovary
7	chr3:50378800-50382800	Weak transcription	HMEC	breast
8	chr3:50378800-50382800	Weak transcription	HSMMtube	muscle
9	chr3:50379000-50382400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:50379000-50382400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:50379000-50382400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:50379000-50382600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:50379000-50382600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:50379000-50382800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:50379000-50382800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:50379000-50382800	Weak transcription	Left Ventricle	heart
17	chr3:50379000-50382800	Weak transcription	Thymus	Thymus
18	chr3:50379000-50382800	Weak transcription	NHEK	skin
19	chr3:50379000-50383000	Weak transcription	Brain Substantia Nigra	brain
20	chr3:50379000-50386800	Weak transcription	Small Intestine	intestine
21	chr3:50379200-50381200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:50379200-50381600	Enhancers	K562	blood
23	chr3:50379200-50382400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:50379200-50382400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:50379200-50382400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:50379200-50382400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:50379200-50382400	Weak transcription	Brain Anterior Caudate	brain
28	chr3:50379200-50382400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr3:50379200-50382600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr3:50379200-50382600	Weak transcription	Liver	Liver
31	chr3:50379200-50382600	Weak transcription	Colonic Mucosa	Colon
32	chr3:50379200-50382600	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:50379200-50382600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:50379200-50382600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:50379200-50382600	Weak transcription	NHLF	lung
36	chr3:50379200-50382600	Weak transcription	Osteobl	bone
37	chr3:50379200-50382800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:50379200-50382800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:50379200-50382800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr3:50379200-50382800	Weak transcription	Right Atrium	heart
41	chr3:50379200-50383000	Weak transcription	Primary T cells from cord blood	blood
42	chr3:50379200-50383000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:50379400-50381000	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr3:50379400-50381000	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr3:50379400-50382400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr3:50379400-50382400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr3:50379400-50382400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:50379400-50382600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:50379400-50382600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr3:50379400-50382600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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