Variant report

Variant	rs2254668
Chromosome Location	chr6:11741825-11741826
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:11733831..11736245-chr6:11739870..11742383,2	K562	blood:
2	chr6:11740535..11742898-chr6:11758594..11760126,2	K562	blood:
3	chr6:11734066..11736149-chr6:11741564..11743376,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111863	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs169791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs172405	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2013368	0.94[CHB][hapmap];0.83[CHD][hapmap]
rs2076184	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs210892	1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs210901	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs210902	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs210906	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs210924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235398	0.82[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2235399	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2235400	0.82[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2235401	0.82[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2235402	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235403	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235405	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235407	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235409	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235413	0.94[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2235420	0.94[CHB][hapmap]
rs2254655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281126	0.82[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294417	0.95[GIH][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2294423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294424	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3734273	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs4713831	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6927223	0.82[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6933892	0.83[CHB][hapmap]
rs6934084	0.83[CHB][hapmap]
rs926364	0.94[CHB][hapmap]
rs932343	0.83[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs932344	0.83[CHB][hapmap]
rs9368864	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9380504	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394268	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs9469986	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	esv2758036	chr6:11679753-11822351	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759407	chr6:11679753-11822351	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv428470	chr6:11686198-11747850	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11719400-11762200	Weak transcription	Colonic Mucosa	Colon
2	chr6:11723600-11744200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:11725200-11748600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:11726400-11744600	Weak transcription	Right Atrium	heart
5	chr6:11732400-11744800	Weak transcription	Fetal Intestine Small	intestine
6	chr6:11732400-11750400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:11732800-11750400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:11734600-11745000	Weak transcription	HSMMtube	muscle
9	chr6:11735200-11744600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:11735600-11743200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr6:11735600-11754800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:11736200-11744600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:11736200-11752400	Weak transcription	NHEK	skin
14	chr6:11736200-11754800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:11736600-11750600	Weak transcription	Stomach Mucosa	stomach
16	chr6:11737600-11744800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:11738000-11743200	Weak transcription	Ovary	ovary
18	chr6:11738000-11743800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:11738600-11762000	Weak transcription	Gastric	stomach
20	chr6:11738800-11743600	Weak transcription	Pancreas	Pancrea
21	chr6:11739000-11742400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:11739000-11755000	Weak transcription	HMEC	breast
23	chr6:11739200-11744600	Weak transcription	Adipose Nuclei	Adipose
24	chr6:11739600-11743000	Weak transcription	Small Intestine	intestine
25	chr6:11739600-11751800	Weak transcription	HUVEC	blood vessel
26	chr6:11740400-11743800	Weak transcription	K562	blood
27	chr6:11741400-11742000	Enhancers	HSMM	muscle
28	chr6:11741600-11745400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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