Variant report

Variant	rs2566347
Chromosome Location	chr3:158491377-158491378
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:158439811..158443418-chr3:158489187..158492099,4	MCF-7	breast:
2	chr3:158485915..158488548-chr3:158489974..158493144,3	MCF-7	breast:
3	chr3:158486963..158488683-chr3:158490589..158492252,2	MCF-7	breast:
4	chr3:158489358..158491459-chr3:158497212..158500197,2	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10513528	0.87[YRI][hapmap]
rs12489730	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12491877	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12495962	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12497488	1.00[ASN][1000 genomes]
rs1430413	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1430414	1.00[ASN][1000 genomes]
rs1560417	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560418	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829365	0.87[ASN][1000 genomes]
rs17630980	0.82[JPT][hapmap]
rs17642769	0.95[ASN][1000 genomes]
rs17643171	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17643252	0.97[ASN][1000 genomes]
rs17643483	0.97[ASN][1000 genomes]
rs17643581	0.97[ASN][1000 genomes]
rs17643860	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17643917	0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs17699478	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[ASN][1000 genomes]
rs17699526	0.95[ASN][1000 genomes]
rs17699997	0.97[ASN][1000 genomes]
rs17700122	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[ASN][1000 genomes]
rs17700475	1.00[ASN][1000 genomes]
rs2279561	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[ASN][1000 genomes]
rs2279562	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[ASN][1000 genomes]
rs2307064	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[ASN][1000 genomes]
rs34690420	1.00[ASN][1000 genomes]
rs3863076	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41434057	0.86[YRI][hapmap]
rs55678388	0.97[ASN][1000 genomes]
rs55705231	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs55717824	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs55776609	0.93[ASN][1000 genomes]
rs56023805	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56078503	0.98[ASN][1000 genomes]
rs56105525	1.00[ASN][1000 genomes]
rs56152025	0.97[ASN][1000 genomes]
rs56235582	0.98[ASN][1000 genomes]
rs56261306	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56318834	0.97[ASN][1000 genomes]
rs57262841	1.00[ASN][1000 genomes]
rs59163359	1.00[ASN][1000 genomes]
rs59173444	0.90[ASN][1000 genomes]
rs60203196	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61138408	1.00[ASN][1000 genomes]
rs61794798	0.97[ASN][1000 genomes]
rs61794799	0.97[ASN][1000 genomes]
rs61794818	0.98[ASN][1000 genomes]
rs61794821	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61794822	1.00[ASN][1000 genomes]
rs61794833	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61794834	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61794835	0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs61794858	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61794859	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61796760	0.85[ASN][1000 genomes]
rs61796762	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61796764	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61796766	0.83[ASN][1000 genomes]
rs61796768	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61796770	0.98[ASN][1000 genomes]
rs6441221	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[ASN][1000 genomes]
rs6761989	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6783610	0.97[ASN][1000 genomes]
rs6792908	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73158361	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7624420	0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs7624702	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv877693	chr3:158470321-158583004	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv1006146	chr3:158475824-158625778	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv592123	chr3:158477796-158625128	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv1002514	chr3:158484027-158673414	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised 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	14 gene(s)	inside rSNPs	diseases
14	nsv536778	chr3:158484027-158673414	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2566347	RSRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158479600-158495600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr3:158485600-158495800	Enhancers	Fetal Intestine Small	intestine
3	chr3:158486400-158494200	Weak transcription	Gastric	stomach
4	chr3:158486600-158494200	Weak transcription	Pancreas	Pancrea
5	chr3:158486800-158518200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:158487000-158491800	Weak transcription	Fetal Brain Male	brain
7	chr3:158487400-158496600	Enhancers	Fetal Lung	lung
8	chr3:158488400-158492000	Weak transcription	Aorta	Aorta
9	chr3:158488400-158493400	Weak transcription	Lung	lung
10	chr3:158488400-158493600	Weak transcription	Left Ventricle	heart
11	chr3:158488400-158501000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:158488600-158491400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:158488800-158494400	Weak transcription	Osteobl	bone
14	chr3:158489200-158495000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:158489200-158508800	Weak transcription	Primary T cells from cord blood	blood
16	chr3:158489400-158492800	Enhancers	Fetal Intestine Large	intestine
17	chr3:158489800-158491400	Weak transcription	Fetal Stomach	stomach
18	chr3:158489800-158494400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:158489800-158495200	Weak transcription	Colonic Mucosa	Colon
20	chr3:158489800-158495200	Weak transcription	Small Intestine	intestine
21	chr3:158489800-158500600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:158490000-158501000	Weak transcription	Ovary	ovary
23	chr3:158490200-158492000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr3:158490200-158493200	Weak transcription	HepG2	liver
25	chr3:158490200-158497800	Weak transcription	Hela-S3	cervix
26	chr3:158490400-158491400	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:158490400-158491600	Weak transcription	A549	lung
28	chr3:158490400-158494200	Weak transcription	Right Atrium	heart
29	chr3:158490600-158491800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:158490600-158492000	Weak transcription	HMEC	breast
31	chr3:158490800-158493200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:158491000-158491800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:158491000-158493400	Enhancers	Fetal Kidney	kidney
34	chr3:158491200-158491400	Enhancers	K562	blood
35	chr3:158491200-158491800	Enhancers	Adipose Nuclei	Adipose
36	chr3:158491200-158493000	Enhancers	NHLF	lung
37	chr3:158491200-158493600	Enhancers	Fetal Muscle Leg	muscle
38	chr3:158491200-158493600	Enhancers	Rectal Smooth Muscle	rectum
39	chr3:158491200-158494400	Weak transcription	Placenta	Placenta

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