Variant report

Variant	rs3212588
Chromosome Location	chr5:52369495-52369496
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	chr5:52240942..52242706-chr5:52367816..52370164,2	MCF-7	breast:

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10051425	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10051483	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10055919	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10058715	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10065574	0.94[EUR][1000 genomes]
rs10065693	0.83[EUR][1000 genomes]
rs1042324	0.90[CEU][hapmap];0.86[GIH][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10471829	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10471830	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10513009	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1139484	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13356629	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13357783	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1445940	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16880872	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16880873	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16880892	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1801106	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2193969	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2233214	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287873	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2303120	0.95[EUR][1000 genomes]
rs2303125	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28413530	0.89[ASN][1000 genomes]
rs28841614	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2910966	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2974984	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3021373	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3212327	0.89[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212429	0.89[ASN][1000 genomes]
rs3212444	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212468	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212487	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212491	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3212492	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3212493	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3212497	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212498	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3212503	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3212504	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212515	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212523	0.89[CEU][hapmap];0.86[GIH][hapmap];0.93[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3212526	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212528	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212529	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212536	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3212539	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3212543	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3212544	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212545	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3212546	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212548	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212558	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212567	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212568	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212569	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212570	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212573	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212579	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212580	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212582	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212583	0.88[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212584	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212585	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212586	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3212593	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212606	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212607	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212612	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212613	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212615	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212628	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212629	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212630	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212633	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212634	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212635	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212643	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3213805	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797474	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3815755	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7446448	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7700416	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7737412	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs875657	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv880389	chr5:52333420-52375199	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv881388	chr5:52339234-52375536	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv881626	chr5:52350521-52370174	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv880601	chr5:52350521-52375927	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv598168	chr5:52355516-52373810	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv881522	chr5:52357916-52370521	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv880866	chr5:52358262-52378295	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv880427	chr5:52363961-52370174	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv881336	chr5:52366284-52374088	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv881091	chr5:52366284-52375199	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv881684	chr5:52366905-52376916	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv881048	chr5:52367956-52370174	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv881520	chr5:52368472-52370521	Weak transcription Genic enhancers Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv881446	chr5:52368472-52375199	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52333800-52369800	Weak transcription	Colonic Mucosa	Colon
2	chr5:52333800-52392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr5:52334800-52380800	Weak transcription	Stomach Mucosa	stomach
4	chr5:52334800-52391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:52337400-52370200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr5:52341200-52396400	Strong transcription	HMEC	breast
8	chr5:52341400-52396400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:52342600-52383800	Strong transcription	NHEK	skin
10	chr5:52343400-52392800	Weak transcription	Left Ventricle	heart
11	chr5:52346200-52386800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr5:52347200-52370000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr5:52347600-52387000	Weak transcription	Fetal Stomach	stomach
14	chr5:52347800-52395000	Weak transcription	Psoas Muscle	Psoas
15	chr5:52348600-52371000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr5:52348600-52394800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr5:52349000-52370200	Weak transcription	Dnd41	blood
18	chr5:52349400-52379600	Weak transcription	Fetal Muscle Leg	muscle
19	chr5:52349600-52371400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr5:52352400-52379200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr5:52352400-52389800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:52354200-52372000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr5:52355600-52371000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr5:52356800-52370800	Weak transcription	Brain Anterior Caudate	brain
25	chr5:52356800-52394000	Weak transcription	Fetal Kidney	kidney
26	chr5:52357200-52371400	Weak transcription	Gastric	stomach
27	chr5:52357400-52370400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr5:52359400-52380000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr5:52360200-52388800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:52360600-52374200	Strong transcription	Hela-S3	cervix
31	chr5:52361200-52392800	Weak transcription	Small Intestine	intestine
32	chr5:52362200-52387800	Strong transcription	HepG2	liver
33	chr5:52362400-52382400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:52363200-52376400	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr5:52363400-52382600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr5:52364200-52374000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr5:52364600-52371200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr5:52365800-52394800	Weak transcription	Right Ventricle	heart
39	chr5:52366000-52382800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:52367400-52386200	Strong transcription	HUVEC	blood vessel
41	chr5:52367400-52388000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr5:52367600-52381200	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr5:52367600-52385000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr5:52367800-52370200	Weak transcription	Osteobl	bone
45	chr5:52367800-52374200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr5:52367800-52386000	Strong transcription	NH-A	brain
47	chr5:52368000-52370600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr5:52368000-52386200	Weak transcription	Aorta	Aorta
49	chr5:52368200-52370200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr5:52368200-52371200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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