Variant report

Variant	rs717961
Chromosome Location	chr17:59804480-59804481
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:59803962..59807532-chr20:45986269..45989123,3	MCF-7	breast:
2	chr1:206882608..206885452-chr17:59803291..59806150,2	MCF-7	breast:
3	chr17:59802918..59807240-chr17:59907754..59912579,5	MCF-7	breast:
4	chr17:59802319..59804545-chr20:50350734..50353080,2	MCF-7	breast:
5	chr17:59802662..59805086-chr17:59913603..59915717,2	MCF-7	breast:
6	chr17:59804101..59807037-chr17:59831514..59833656,2	MCF-7	breast:
7	chr17:59713558..59715290-chr17:59804432..59807053,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000215444	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1015771	0.95[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs10221278	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs10438771	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs10468558	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs10515206	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[EUR][1000 genomes]
rs10515207	0.94[CEU][hapmap];0.88[CHB][hapmap];0.84[EUR][1000 genomes]
rs10515211	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs10853038	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[EUR][1000 genomes]
rs10853039	0.87[EUR][1000 genomes]
rs11079445	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs11079446	0.86[EUR][1000 genomes]
rs11079448	0.86[EUR][1000 genomes]
rs11650471	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs11651510	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11658539	0.80[EUR][1000 genomes]
rs11871753	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs12449319	0.86[EUR][1000 genomes]
rs12450027	0.85[EUR][1000 genomes]
rs12451862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12453293	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12453801	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs12453935	0.80[MEX][hapmap]
rs12453966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12603485	0.85[EUR][1000 genomes]
rs12603617	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs12937232	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12949659	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs12950438	0.87[EUR][1000 genomes]
rs1468577	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs1541346	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs16945500	0.86[EUR][1000 genomes]
rs17532528	0.85[EUR][1000 genomes]
rs1978244	0.90[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs1990337	0.80[EUR][1000 genomes]
rs1990338	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs2024188	0.87[EUR][1000 genomes]
rs2040608	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs2109252	0.87[EUR][1000 genomes]
rs2109254	0.87[EUR][1000 genomes]
rs2109255	0.87[EUR][1000 genomes]
rs2158006	0.83[EUR][1000 genomes]
rs2159450	0.87[EUR][1000 genomes]
rs2188731	0.85[EUR][1000 genomes]
rs2191247	0.86[EUR][1000 genomes]
rs2191249	0.95[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs2214184	0.88[EUR][1000 genomes]
rs2378874	0.85[EUR][1000 genomes]
rs2378875	0.85[EUR][1000 genomes]
rs2378884	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2378902	0.87[EUR][1000 genomes]
rs2378905	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs2378906	0.80[EUR][1000 genomes]
rs28571892	0.87[EUR][1000 genomes]
rs2890012	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[EUR][1000 genomes]
rs2890013	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[EUR][1000 genomes]
rs2890021	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs36031690	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4309463	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4343344	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4580256	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4968444	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[EUR][1000 genomes]
rs4968447	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4968577	0.85[EUR][1000 genomes]
rs4968579	0.86[EUR][1000 genomes]
rs4968580	0.86[EUR][1000 genomes]
rs4968582	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs4968584	0.86[EUR][1000 genomes]
rs4968585	0.86[EUR][1000 genomes]
rs4968588	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4988351	0.81[EUR][1000 genomes]
rs55797010	0.86[EUR][1000 genomes]
rs56284136	0.86[EUR][1000 genomes]
rs57099937	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57393813	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61599541	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62068837	0.80[EUR][1000 genomes]
rs62070615	0.86[EUR][1000 genomes]
rs62070616	0.86[EUR][1000 genomes]
rs62070617	0.86[EUR][1000 genomes]
rs62070624	0.82[EUR][1000 genomes]
rs6504066	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6504068	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs6504070	0.82[EUR][1000 genomes]
rs6504071	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs6504072	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs67273191	0.85[EUR][1000 genomes]
rs67938055	0.86[EUR][1000 genomes]
rs717962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207074	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207881	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs7208704	0.94[CEU][hapmap]
rs7212172	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs7212423	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7213329	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs7213470	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7213587	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7213759	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7214884	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs7215784	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs7216011	0.80[EUR][1000 genomes]
rs7216756	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs7216824	0.80[EUR][1000 genomes]
rs7217206	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs7217292	0.87[EUR][1000 genomes]
rs7220688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7220719	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7222799	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs72841508	0.86[EUR][1000 genomes]
rs8074949	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8075370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8075397	0.88[EUR][1000 genomes]
rs8077088	0.80[EUR][1000 genomes]
rs8078977	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs8182296	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9303449	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs9807012	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9895987	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs9896013	0.85[EUR][1000 genomes]
rs9897121	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs9897450	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9897928	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs9900559	0.80[EUR][1000 genomes]
rs9901428	0.85[EUR][1000 genomes]
rs9902995	0.95[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs9903041	0.85[EUR][1000 genomes]
rs9904292	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs9904294	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9905870	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9906313	0.95[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs9907299	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs991378	0.80[EUR][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	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv908673	chr17:59767501-59926645	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
3	nsv908674	chr17:59800827-59899790	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
4	esv3335472	chr17:59803168-59821322	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs717961	BRIP1	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59766000-59819000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr17:59778200-59805800	Weak transcription	Thymus	Thymus
3	chr17:59781600-59835400	Weak transcription	Hela-S3	cervix
4	chr17:59784400-59815200	Weak transcription	HMEC	breast
5	chr17:59786600-59815400	Weak transcription	Fetal Thymus	thymus
6	chr17:59792000-59815200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr17:59793200-59819400	Weak transcription	NH-A	brain
8	chr17:59793600-59821200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr17:59794200-59815200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr17:59794200-59819600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr17:59794400-59815200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr17:59794400-59816200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr17:59794400-59848200	Weak transcription	HUVEC	blood vessel
14	chr17:59794600-59807200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr17:59794800-59806000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr17:59794800-59815200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr17:59796200-59805600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr17:59796200-59805800	Weak transcription	A549	lung
19	chr17:59796200-59814400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr17:59797400-59817600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr17:59797600-59813000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr17:59798400-59815000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr17:59798800-59816400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr17:59800800-59814400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr17:59801000-59815400	Weak transcription	HepG2	liver
26	chr17:59801200-59817400	Weak transcription	Small Intestine	intestine
27	chr17:59801600-59805800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr17:59801600-59815000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr17:59801600-59816200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr17:59802000-59808600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr17:59803000-59804600	Strong transcription	Dnd41	blood
32	chr17:59803000-59808000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr17:59803400-59807600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr17:59804000-59805800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr17:59804200-59804800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr17:59804200-59814400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr17:59804200-59818800	Weak transcription	Brain Germinal Matrix	brain
38	chr17:59804200-59847400	Weak transcription	K562	blood

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