Variant report

Variant	rs3212630
Chromosome Location	chr5:52381162-52381163
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52285755..52287338-chr5:52380121..52382244,2	MCF-7	breast:
2	chr5:52380023..52382035-chr5:52385112..52387338,2	K562	blood:

Variant related genes	Relation type
ENSG00000272123	Chromatin interaction
ENSG00000249899	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10051425	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10051483	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10055919	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10058715	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10065574	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10065693	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1042324	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10471829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10471830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513009	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1139484	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13356629	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13357783	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1445940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16880872	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16880873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16880892	0.89[CEU][hapmap]
rs1801106	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2193969	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2233214	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2287873	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303120	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303125	1.00[EUR][1000 genomes]
rs28841614	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2910966	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2974984	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3021373	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212429	0.90[AFR][1000 genomes]
rs3212444	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3212468	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3212487	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3212491	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3212492	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212493	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212497	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3212498	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212503	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212504	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3212515	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3212523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3212526	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3212528	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3212529	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3212536	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212539	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212543	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212544	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212545	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3212546	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212548	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212558	0.97[EUR][1000 genomes]
rs3212567	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212568	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212569	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212570	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212573	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212579	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212580	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212582	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212584	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212585	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212586	0.95[EUR][1000 genomes]
rs3212588	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212593	1.00[EUR][1000 genomes]
rs3212606	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212607	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212612	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212613	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212615	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212628	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212633	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3212634	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212635	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3212643	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213805	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs3797474	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815755	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7446448	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs7700416	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7737412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv881652	chr5:52323568-52385312	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv880598	chr5:52379277-52382904	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52333800-52392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr5:52334800-52391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:52341200-52396400	Strong transcription	HMEC	breast
5	chr5:52341400-52396400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:52342600-52383800	Strong transcription	NHEK	skin
7	chr5:52343400-52392800	Weak transcription	Left Ventricle	heart
8	chr5:52346200-52386800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr5:52347600-52387000	Weak transcription	Fetal Stomach	stomach
10	chr5:52347800-52395000	Weak transcription	Psoas Muscle	Psoas
11	chr5:52348600-52394800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:52352400-52389800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:52356800-52394000	Weak transcription	Fetal Kidney	kidney
14	chr5:52360200-52388800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:52361200-52392800	Weak transcription	Small Intestine	intestine
16	chr5:52362200-52387800	Strong transcription	HepG2	liver
17	chr5:52362400-52382400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:52363400-52382600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr5:52365800-52394800	Weak transcription	Right Ventricle	heart
20	chr5:52366000-52382800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:52367400-52386200	Strong transcription	HUVEC	blood vessel
22	chr5:52367400-52388000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr5:52367600-52381200	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr5:52367600-52385000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:52367800-52386000	Strong transcription	NH-A	brain
26	chr5:52368000-52386200	Weak transcription	Aorta	Aorta
27	chr5:52369000-52392800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:52369400-52382600	Weak transcription	Brain Angular Gyrus	brain
29	chr5:52369400-52383600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:52370400-52394600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr5:52370400-52404600	Weak transcription	Brain Germinal Matrix	brain
32	chr5:52372000-52382600	Weak transcription	Brain Anterior Caudate	brain
33	chr5:52372000-52394800	Weak transcription	Colonic Mucosa	Colon
34	chr5:52372000-52394800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr5:52372200-52382600	Weak transcription	Lung	lung
36	chr5:52372200-52382800	Weak transcription	Spleen	Spleen
37	chr5:52372200-52384800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr5:52372200-52392800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr5:52372200-52394800	Weak transcription	Gastric	stomach
40	chr5:52372200-52394800	Weak transcription	Pancreas	Pancrea
41	chr5:52372400-52385000	Weak transcription	Osteobl	bone
42	chr5:52372400-52404400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr5:52372800-52386400	Weak transcription	NHDF-Ad	bronchial
44	chr5:52373000-52385600	Weak transcription	Ovary	ovary
45	chr5:52373000-52387000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:52373400-52382600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr5:52373800-52386200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:52374200-52382600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:52374200-52392800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr5:52375000-52382400	Weak transcription	Brain Cingulate Gyrus	brain

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