Variant report

Variant	rs10946891
Chromosome Location	chr6:26973215-26973216
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	chr6:26972821..26975346-chr6:26986286..26989027,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238621	Chromatin interaction
ENSG00000224843	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10456351	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10456352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10946892	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10946893	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10946897	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10946898	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11754305	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11756275	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12189814	0.93[ASW][hapmap];0.83[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs12193875	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12201034	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12201393	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209886	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211984	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12213438	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12523820	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12527111	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12527231	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12661756	0.89[GIH][hapmap];0.87[TSI][hapmap]
rs13212021	0.89[ASN][1000 genomes]
rs13217675	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2022272	0.84[JPT][hapmap];0.83[MEX][hapmap]
rs2057348	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2142685	0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2393915	0.80[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs35691005	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3999229	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4269366	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4358615	0.81[CHB][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.87[TSI][hapmap]
rs4403259	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4422620	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4424065	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4434464	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4476823	0.85[ASN][1000 genomes]
rs4509113	0.89[ASN][1000 genomes]
rs4583981	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];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4713066	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713069	0.85[JPT][hapmap]
rs62401067	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62402054	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456767	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6456768	0.80[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6910264	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6921388	0.90[JPT][hapmap]
rs6930508	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6937880	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7451149	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7739845	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7744759	0.84[JPT][hapmap]
rs7747454	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7768407	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9379955	0.80[EUR][1000 genomes]
rs9379956	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9379958	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9393789	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9393790	0.84[JPT][hapmap]
rs9461330	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9467936	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9467978	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs994691	0.80[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	esv2758038	chr6:26695219-27095714	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
3	esv2759410	chr6:26695219-27095714	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
4	nsv1029124	chr6:26825468-27109774	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	244 gene(s)	inside rSNPs	diseases
5	nsv469610	chr6:26841083-26999230	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription 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	23 gene(s)	inside rSNPs	diseases
6	nsv482509	chr6:26841083-26999230	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv471636	chr6:26841084-27038175	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	esv19090	chr6:26843813-26983456	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv469675	chr6:26848950-27015598	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv482429	chr6:26848950-27015598	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv830616	chr6:26859097-27030476	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	esv1793267	chr6:26864376-26987405	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	esv1811325	chr6:26869783-26987405	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
14	esv1795502	chr6:26873947-26983005	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	esv1795223	chr6:26877074-26987205	Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	esv1809024	chr6:26877074-26987205	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	esv1810582	chr6:26889428-26990246	Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
18	nsv469625	chr6:26893739-27038175	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
19	nsv482537	chr6:26893739-27038175	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
20	esv15177	chr6:26916403-26987915	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs10946891	HCG11	Cis_1M	lymphoblastoid	RTeQTL
rs10946891	BTN3A3	cis	cerebellum	SCAN
rs10946891	BTN3A2	cis	lymphoblastoid	seeQTL
rs10946891	HIST1H2BH	cis	cerebellum	SCAN
rs10946891	RP11-457M11.5	cis	Heart Left Ventricle	GTEx
rs10946891	RP11-457M11.5	cis	Artery Tibial	GTEx
rs10946891	RP11-457M11.5	cis	Thyroid	GTEx
rs10946891	RP11-457M11.5	cis	Stomach	GTEx
rs10946891	RP11-457M11.5	cis	Esophagus Muscularis	GTEx
rs10946891	BTN2A1	cis	parietal	SCAN
rs10946891	RP11-457M11.5	cis	Esophagus Mucosa	GTEx
rs10946891	RP11-457M11.5	cis	lung	GTEx
rs10946891	HIST1H2BM	cis	cerebellum	SCAN
rs10946891	RP11-457M11.5	cis	Nerve Tibial	GTEx
rs10946891	RP11-457M11.5	cis	Skin Sun Exposed Lower leg	GTEx
rs10946891	RP11-457M11.5	cis	Whole Blood	GTEx
rs10946891	HMGN4	cis	lymphoblastoid	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26969400-26975000	Weak transcription	Ovary	ovary
2	chr6:26972600-26979200	Weak transcription	Brain Substantia Nigra	brain
3	chr6:26973200-26973400	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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