Variant report

Variant	rs684977
Chromosome Location	chr11:59961144-59961145
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:59590156..59591101-chr11:59960804..59961684,4	MCF-7	breast:
2	chr11:59915996..59916912-chr11:59960707..59961353,2	K562	blood:
3	chr11:59936023..59937006-chr11:59960779..59961684,2	MCF-7	breast:
4	chr11:59885540..59886539-chr11:59960885..59961593,3	MCF-7	breast:

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10750930	0.89[JPT][hapmap]
rs1286182	0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1294440	0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs1303617	0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1303618	0.96[EUR][1000 genomes]
rs1303619	0.96[EUR][1000 genomes]
rs1303620	0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1303622	0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1315507	0.96[EUR][1000 genomes]
rs1426252	0.87[ASN][1000 genomes]
rs1441585	0.90[JPT][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs2081546	0.87[ASN][1000 genomes]
rs2243987	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2433240	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2847662	0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs474888	0.96[EUR][1000 genomes]
rs475494	0.96[EUR][1000 genomes]
rs475812	0.89[JPT][hapmap];0.96[EUR][1000 genomes]
rs477352	0.96[EUR][1000 genomes]
rs485682	0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs489297	0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs500886	0.96[EUR][1000 genomes]
rs500888	0.96[EUR][1000 genomes]
rs512548	0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs512555	0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs519743	0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs523806	0.96[EUR][1000 genomes]
rs524755	0.96[EUR][1000 genomes]
rs524995	0.84[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs528421	0.96[EUR][1000 genomes]
rs535413	0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs541468	0.96[EUR][1000 genomes]
rs542665	0.96[EUR][1000 genomes]
rs546840	0.96[EUR][1000 genomes]
rs548515	0.96[EUR][1000 genomes]
rs549633	0.96[EUR][1000 genomes]
rs562442	0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs562637	0.96[EUR][1000 genomes]
rs569108	0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs571582	0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs572084	0.96[EUR][1000 genomes]
rs573305	0.96[EUR][1000 genomes]
rs574060	0.96[EUR][1000 genomes]
rs574700	0.82[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs575103	0.96[EUR][1000 genomes]
rs575930	0.96[EUR][1000 genomes]
rs576295	0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs576483	0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs576616	0.96[EUR][1000 genomes]
rs578269	0.82[JPT][hapmap];0.96[EUR][1000 genomes]
rs581818	1.00[ASN][1000 genomes]
rs582407	0.87[ASN][1000 genomes]
rs585540	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs587634	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs588448	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs590351	0.97[ASN][1000 genomes]
rs590532	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs592496	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs594414	0.87[ASN][1000 genomes]
rs595014	0.87[ASN][1000 genomes]
rs596788	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597982	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs598862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600194	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs605820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs607639	0.87[ASN][1000 genomes]
rs613548	0.84[ASN][1000 genomes]
rs613629	0.87[ASN][1000 genomes]
rs615405	0.87[ASN][1000 genomes]
rs620368	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs624233	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636988	0.87[ASN][1000 genomes]
rs638872	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641051	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641829	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs642426	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs646924	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs649234	0.86[ASN][1000 genomes]
rs650777	0.87[ASN][1000 genomes]
rs650853	0.85[ASN][1000 genomes]
rs650926	0.87[ASN][1000 genomes]
rs653285	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs654443	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs661376	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs662674	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs668095	0.92[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs668134	0.92[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs670925	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs672218	0.87[ASN][1000 genomes]
rs674971	0.87[ASN][1000 genomes]
rs675316	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs675452	0.84[ASN][1000 genomes]
rs680699	0.97[ASN][1000 genomes]
rs682025	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs682739	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73485360	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468579	chr11:59814287-59975400	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv555150	chr11:59814287-59975400	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv832174	chr11:59909267-60073908	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs684977	MS4A6A	cis	multi-tissue	Pritchard

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59950800-59961200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:59960200-59965000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr11:59960400-59961400	ZNF genes & repeats	GM12878-XiMat	blood
4	chr11:59960400-59962800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr11:59960400-59965400	Enhancers	Dnd41	blood
6	chr11:59961000-59961200	Flanking Active TSS	HUVEC	blood vessel
7	chr11:59961000-59961200	Flanking Active TSS	K562	blood
8	chr11:59961000-59962400	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr11:59961000-59962400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr11:59961000-59962400	Enhancers	HMEC	breast
11	chr11:59961000-59963600	Enhancers	Fetal Intestine Large	intestine
12	chr11:59961000-59963800	Enhancers	Primary B cells from cord blood	blood
13	chr11:59961000-59965000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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