Variant report

Variant	rs6456674
Chromosome Location	chr6:25347940-25347941
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10946762	0.82[ASN][1000 genomes]
rs11491476	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11965829	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11967836	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12664362	0.82[ASN][1000 genomes]
rs16890448	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16890454	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56930318	0.93[ASN][1000 genomes]
rs57899991	0.93[ASN][1000 genomes]
rs60384851	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456670	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456671	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6456672	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456675	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456676	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6456677	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6932311	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73399971	0.93[ASN][1000 genomes]
rs7750609	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7766986	0.82[AFR][1000 genomes]
rs7770521	0.89[ASN][1000 genomes]
rs9461141	0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9461142	0.93[ASN][1000 genomes]
rs9461143	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9461144	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9467474	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9986335	0.90[ASN][1000 genomes]
rs9986525	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9986604	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9986608	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv601168	chr6:25346334-25393306	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv275059	chr6:25346985-25351263	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25335200-25359800	Weak transcription	Thymus	Thymus
2	chr6:25336800-25350200	Weak transcription	Lung	lung
3	chr6:25336800-25354600	Weak transcription	Right Atrium	heart
4	chr6:25337400-25357800	Weak transcription	NHEK	skin
5	chr6:25340000-25349400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:25341000-25352800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:25341000-25359400	Weak transcription	Pancreas	Pancrea
8	chr6:25342400-25350600	Weak transcription	HSMMtube	muscle
9	chr6:25342800-25351800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:25342800-25354400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:25343000-25352600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:25343600-25348200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:25343800-25350600	Weak transcription	Fetal Intestine Large	intestine
14	chr6:25343800-25354000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:25344000-25350600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:25344200-25349400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:25345400-25349200	Weak transcription	Aorta	Aorta
18	chr6:25346600-25349400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:25346600-25349400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:25346600-25350400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:25346600-25359400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:25346800-25350600	Weak transcription	Small Intestine	intestine
23	chr6:25346800-25351800	Weak transcription	Fetal Intestine Small	intestine
24	chr6:25346800-25352800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr6:25346800-25359200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr6:25347000-25350400	Weak transcription	Fetal Lung	lung
27	chr6:25347000-25352400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:25347000-25354200	Weak transcription	Stomach Mucosa	stomach
29	chr6:25347000-25359400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:25347200-25351600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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