Variant report

Variant	rs11754288
Chromosome Location	chr6:25776949-25776950
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	chr6:25775506..25777112-chr6:25883078..25885992,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1165151	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1165153	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1165154	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1165160	0.81[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap]
rs1165176	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap]
rs1165177	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1165178	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1165182	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1165195	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1165196	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1165199	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1165205	0.81[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap]
rs1165206	0.92[JPT][hapmap]
rs1165207	0.81[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap]
rs1165209	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1165213	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1165215	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1177442	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1183200	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1183201	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1184803	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1184804	0.80[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap]
rs1185153	0.88[CHB][hapmap]
rs1185567	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1185568	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1185569	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap]
rs1185978	0.81[CHB][hapmap]
rs12201071	0.82[ASN][1000 genomes]
rs12209125	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12212049	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12662869	0.85[JPT][hapmap]
rs13197514	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13197601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1359232	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1747522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1892249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2328895	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2762353	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2817188	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35720558	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3757130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3757131	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3799340	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799344	0.96[CEU][hapmap];0.98[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs3799352	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4145221	0.82[ASN][1000 genomes]
rs566530	0.90[CHB][hapmap]
rs6456693	1.00[JPT][hapmap]
rs6909187	0.86[EUR][1000 genomes]
rs765285	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9393670	1.00[JPT][hapmap]
rs942379	0.81[CEU][hapmap];0.90[CHB][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap]

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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv427747	chr6:25641380-25908218	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv969355	chr6:25733459-25779530	Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Blood metabolite levels	24816252	GWAS catalog
Cardiovascular disease risk factors	21943158	GWAS catalog

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25758600-25777200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:25762200-25780400	Strong transcription	Liver	Liver
3	chr6:25770800-25780000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:25773800-25777800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:25773800-25788600	Weak transcription	Pancreas	Pancrea
6	chr6:25775000-25781000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:25775000-25781200	Weak transcription	Fetal Intestine Small	intestine
8	chr6:25776600-25780200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:25776800-25777600	Strong transcription	Duodenum Mucosa	Duodenum
10	chr6:25776800-25778200	Strong transcription	Fetal Intestine Large	intestine
11	chr6:25776800-25778200	Enhancers	Placenta	Placenta
12	chr6:25776800-25780000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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