Variant report

Variant	rs3009197
Chromosome Location	chr1:120359998-120359999
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	chr1:120358099..120360727-chr1:144531568..144534050,2	K562	blood:
2	chr1:120333977..120336154-chr1:120357521..120360172,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000201699	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1815687	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1856970	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1856971	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2153675	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2153676	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2185608	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2226084	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2266023	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2363611	0.89[AFR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2487572	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2487573	0.86[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2487575	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2495288	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs2793833	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2994808	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2994809	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2994810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2994811	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2994812	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2994813	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2994814	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2994815	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2994816	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2994817	0.95[AFR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2994818	0.92[AFR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2994819	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2994820	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2994821	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2994822	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3009182	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap]
rs3009184	0.94[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap]
rs3009186	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3009187	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3009189	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3009190	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs3009191	0.87[EUR][1000 genomes]
rs3009192	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3009194	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3009195	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3009196	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3009198	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3009199	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs835565	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs835578	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs844346	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs856658	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs860674	1.00[CEU][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs947268	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs947274	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv915933	chr1:120323527-120471049	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv831226	chr1:120331599-120471049	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv947316	chr1:120355309-120362730	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv533996	chr1:120359524-120471049	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
11	esv3398352	chr1:120359660-120360262	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120356600-120361200	Enhancers	Fetal Intestine Small	intestine
2	chr1:120356800-120361000	Enhancers	Fetal Intestine Large	intestine
3	chr1:120356800-120361200	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr1:120357000-120360800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:120357200-120361000	Enhancers	HepG2	liver
6	chr1:120358400-120360200	Enhancers	Duodenum Mucosa	Duodenum
7	chr1:120358800-120360800	Enhancers	Liver	Liver
8	chr1:120359000-120361000	Enhancers	Rectal Mucosa Donor 29	rectum
9	chr1:120359000-120372200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:120359400-120363000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:120359600-120360800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:120359600-120360800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:120359600-120360800	Weak transcription	Stomach Mucosa	stomach

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