Variant report

Variant	rs12209234
Chromosome Location	chr6:5530197-5530198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12193006	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195596	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197357	1.00[ASN][1000 genomes]
rs12199468	0.86[CEU][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12203435	1.00[ASN][1000 genomes]
rs12203726	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12204218	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204655	1.00[ASN][1000 genomes]
rs12206230	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213022	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196232	1.00[ASN][1000 genomes]
rs13202324	1.00[ASN][1000 genomes]
rs13209186	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17274714	0.90[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34234636	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34669476	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34910355	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35251058	1.00[ASN][1000 genomes]
rs35458062	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35565840	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35940054	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62387165	1.00[ASN][1000 genomes]
rs9504426	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1034607	chr6:5311590-5573514	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv538120	chr6:5311590-5573514	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1023027	chr6:5377308-5556749	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv538121	chr6:5377308-5556749	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1017506	chr6:5443538-5551125	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv883420	chr6:5524393-5584422	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5501000-5550600	Weak transcription	Pancreas	Pancrea
2	chr6:5508000-5547400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:5511200-5546400	Weak transcription	Fetal Intestine Small	intestine
4	chr6:5511400-5540200	Weak transcription	Esophagus	oesophagus
5	chr6:5511400-5568200	Weak transcription	Aorta	Aorta
6	chr6:5514000-5537400	Weak transcription	Left Ventricle	heart
7	chr6:5518600-5550000	Weak transcription	Right Ventricle	heart
8	chr6:5522600-5531400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:5522600-5544600	Weak transcription	Ovary	ovary
10	chr6:5522600-5548000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr6:5522800-5550400	Weak transcription	GM12878-XiMat	blood
12	chr6:5523000-5549000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:5523400-5531200	Weak transcription	Primary T cells from cord blood	blood
14	chr6:5523600-5531400	Weak transcription	Fetal Thymus	thymus
15	chr6:5525200-5547600	Weak transcription	Primary B cells from cord blood	blood
16	chr6:5525400-5531400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:5525800-5531400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:5526200-5531400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr6:5529000-5546800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr6:5529400-5530800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:5529600-5530400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr6:5529600-5530400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:5529800-5530400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:5529800-5530400	Enhancers	H9 Cell Line	embryonic stem cell
25	chr6:5529800-5530800	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr6:5530000-5530200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:5530000-5530400	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr6:5530000-5530400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:5530000-5530400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:5530000-5530600	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr6:5530000-5530600	Enhancers	iPS-20b Cell Line	embryonic stem cell

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