Variant report

Variant	rs4296904
Chromosome Location	chr6:128699502-128699503
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12055766	0.89[JPT][hapmap]
rs1339191	0.94[JPT][hapmap]
rs1339193	0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1339197	0.80[JPT][hapmap]
rs3822945	0.81[CHD][hapmap]
rs57546390	0.91[AMR][1000 genomes]
rs6934873	0.88[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7744436	0.94[JPT][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes]
rs9321119	1.00[GIH][hapmap]
rs9372889	0.81[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9372892	1.00[GIH][hapmap]
rs9385457	0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9388629	1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes]
rs9402037	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9491939	1.00[JPT][hapmap]
rs953549	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs964179	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers 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 miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128679600-128732000	Weak transcription	Left Ventricle	heart
2	chr6:128688800-128706800	Weak transcription	Gastric	stomach
3	chr6:128688800-128738800	Weak transcription	Psoas Muscle	Psoas
4	chr6:128690000-128704400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:128690400-128701800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr6:128691200-128711200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:128691600-128699800	Weak transcription	NHLF	lung
8	chr6:128691600-128730400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr6:128692200-128701000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:128696400-128699600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
11	chr6:128697400-128700400	Weak transcription	Fetal Lung	lung
12	chr6:128697400-128700600	Weak transcription	Ovary	ovary
13	chr6:128697800-128733400	Weak transcription	HSMM	muscle
14	chr6:128698200-128701800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:128698400-128701000	Weak transcription	Brain Substantia Nigra	brain
16	chr6:128698600-128701200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:128698600-128709800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr6:128698800-128700800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:128698800-128701400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr6:128698800-128709000	Weak transcription	Fetal Intestine Small	intestine
21	chr6:128698800-128724000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:128698800-128743200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:128699200-128715000	Weak transcription	HepG2	liver
24	chr6:128699400-128699600	ZNF genes & repeats	NHEK	skin
25	chr6:128699400-128703200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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