Variant report

Variant	rs10061689
Chromosome Location	chr5:74771387-74771388
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:74770863..74773429-chr5:74777117..74779848,3	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10036682	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10038945	0.80[AFR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10041470	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10055011	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10059022	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10067900	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10074747	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10076819	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10077427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10078671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10474437	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12173076	0.86[EUR][1000 genomes]
rs13360099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13361353	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1469051	0.88[EUR][1000 genomes]
rs1553234	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1820049	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1909719	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2287710	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28408106	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28612248	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28668361	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28874007	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34355	0.81[CHD][hapmap]
rs34357	0.81[CHD][hapmap]
rs3804231	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4703671	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4703675	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4704213	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4704229	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56859362	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5744544	0.92[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5744545	0.92[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5744636	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5744667	0.85[YRI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5744704	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5744709	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5744712	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57907925	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58519566	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58841453	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6891560	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633963	0.81[ASN][1000 genomes]
rs72633964	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72633965	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72633966	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72633967	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72633968	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72633969	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633970	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633971	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633972	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72633973	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72633974	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72633975	0.80[AFR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72633976	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72633977	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7356633	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7726478	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs904743	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9293652	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9293654	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9293655	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs979182	0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882193	chr5:74656175-74917862	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv882195	chr5:74678937-74896798	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv882196	chr5:74678937-74917862	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv882197	chr5:74692776-74946455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv882198	chr5:74736065-74896798	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv882199	chr5:74757758-74946455	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10061689	ARSB	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74732000-74787400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:74742400-74794200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:74760400-74776800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:74760400-74792200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:74762200-74805800	Weak transcription	Pancreas	Pancrea
6	chr5:74762600-74778000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:74763200-74787400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr5:74764600-74776600	Weak transcription	Gastric	stomach
9	chr5:74764600-74776600	Weak transcription	Psoas Muscle	Psoas
10	chr5:74764800-74773000	Weak transcription	Thymus	Thymus
11	chr5:74764800-74778000	Weak transcription	Aorta	Aorta
12	chr5:74764800-74778000	Weak transcription	Left Ventricle	heart
13	chr5:74764800-74785800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr5:74764800-74786200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr5:74764800-74798600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:74765200-74795400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr5:74765200-74804600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr5:74765800-74786800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr5:74765800-74787200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr5:74766200-74785600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:74766400-74771400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr5:74766600-74778200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr5:74766600-74785600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:74767000-74779400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:74767200-74774400	Weak transcription	Primary T cells from cord blood	blood
26	chr5:74767200-74778000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr5:74767400-74787000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr5:74767600-74778000	Weak transcription	Fetal Muscle Leg	muscle
29	chr5:74767800-74774200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr5:74768200-74777800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr5:74769000-74771400	Enhancers	Liver	Liver
32	chr5:74769200-74777800	Weak transcription	Fetal Stomach	stomach
33	chr5:74769200-74794000	Weak transcription	Fetal Thymus	thymus
34	chr5:74769400-74772200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr5:74769400-74776600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr5:74769400-74777800	Weak transcription	Fetal Intestine Small	intestine
37	chr5:74769400-74779800	Weak transcription	Fetal Intestine Large	intestine
38	chr5:74769400-74794800	Weak transcription	Stomach Mucosa	stomach
39	chr5:74769600-74772400	Weak transcription	A549	lung
40	chr5:74769600-74775400	Weak transcription	Primary B cells from cord blood	blood
41	chr5:74770200-74773000	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr5:74770200-74773400	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr5:74770200-74773400	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr5:74770200-74773400	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr5:74770400-74805200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr5:74770600-74772000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr5:74770800-74771600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr5:74770800-74773200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr5:74771000-74771600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr5:74771000-74771800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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