Variant report

Variant	rs2235398
Chromosome Location	chr6:11756013-11756014
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:11750475..11752074-chr6:11754495..11757382,2	K562	blood:
2	chr6:11755867..11758010-chr6:11770135..11772213,2	K562	blood:
3	chr6:11718348..11720271-chr6:11754971..11757663,2	K562	blood:
4	chr6:11754440..11757248-chr6:11757537..11760233,3	K562	blood:
5	chr6:11755388..11758313-chr6:11766976..11769042,2	K562	blood:

Variant related genes	Relation type
ENSG00000111863	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs169791	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs172405	0.82[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2013368	0.84[CHB][hapmap]
rs2076184	0.95[JPT][hapmap]
rs210892	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs210901	0.95[JPT][hapmap]
rs210902	0.95[JPT][hapmap]
rs210906	0.95[JPT][hapmap]
rs210924	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs210930	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2235399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2235400	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235401	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2235402	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2235403	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2235405	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2235407	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2235409	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2235413	0.84[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs2235420	0.84[CHB][hapmap]
rs2254655	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2254668	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]
rs2281126	1.00[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2294417	0.95[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2294423	0.82[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2294424	0.82[ASW][hapmap];0.82[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4713831	0.95[JPT][hapmap]
rs6927223	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926364	0.84[CHB][hapmap]
rs932343	0.86[JPT][hapmap]
rs9368864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380504	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9394268	0.95[JPT][hapmap]
rs9469986	0.84[ASW][hapmap];0.82[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11719400-11762200	Weak transcription	Colonic Mucosa	Colon
2	chr6:11738600-11762000	Weak transcription	Gastric	stomach
3	chr6:11752400-11757800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:11753000-11757800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:11753000-11759200	Weak transcription	Stomach Mucosa	stomach
6	chr6:11753000-11760000	Weak transcription	Small Intestine	intestine
7	chr6:11753200-11759200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:11753200-11763800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:11753600-11758000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr6:11754200-11756600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:11754400-11756400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:11754800-11756200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:11754800-11756200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:11754800-11756200	Enhancers	Osteobl	bone
15	chr6:11755000-11756400	Enhancers	Adipose Nuclei	Adipose
16	chr6:11755000-11757800	Weak transcription	Fetal Intestine Small	intestine
17	chr6:11755400-11756200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:11755400-11756200	Enhancers	NHEK	skin
19	chr6:11755400-11759800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr6:11755800-11756800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:11755800-11757800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:11755800-11768400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:11756000-11757600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr6:11756000-11758000	Weak transcription	HMEC	breast

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