Variant report

Variant	rs3778537
Chromosome Location	chr6:1845963-1845964
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:1845499..1849284-chr6:1851999..1854046,3	K562	blood:
2	chr6:1843508..1846277-chr6:1850765..1853357,2	MCF-7	breast:
3	chr6:1839714..1842732-chr6:1843630..1846250,4	MCF-7	breast:
4	chr6:1841908..1843510-chr6:1844738..1846986,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1467594	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1543538	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2281760	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs2296131	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs3778538	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3778540	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs3800091	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3800097	0.96[CEU][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs3800099	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs3800100	0.96[CEU][hapmap];0.85[YRI][hapmap];0.94[EUR][1000 genomes]
rs3800102	0.92[CEU][hapmap]
rs3800103	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs3800104	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs3800106	0.85[CEU][hapmap]
rs3800107	0.92[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3800108	0.86[CEU][hapmap]
rs3800115	0.89[CEU][hapmap]
rs3800121	0.85[CEU][hapmap]
rs3823277	0.96[CEU][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs4959613	0.86[ASN][1000 genomes]
rs6940806	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs9328073	0.85[CEU][hapmap]
rs9378661	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs9391935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9392342	0.85[CEU][hapmap]
rs9405152	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription 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	76 gene(s)	inside rSNPs	diseases
2	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1020603	chr6:1697548-1921374	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv538093	chr6:1697548-1921374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv869043	chr6:1744238-2006788	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv538094	chr6:1757776-1907505	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
9	nsv883383	chr6:1775436-1918572	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv883384	chr6:1787862-1942538	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1019895	chr6:1832936-1882435	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1829800-1856600	Weak transcription	Primary T cells from cord blood	blood
2	chr6:1833400-1856600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:1833600-1846000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:1833600-1849600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:1834000-1848000	Weak transcription	HepG2	liver
6	chr6:1838200-1862200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:1838800-1846000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:1842200-1852200	Weak transcription	Thymus	Thymus
9	chr6:1842400-1850200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:1842800-1846000	Weak transcription	Left Ventricle	heart
11	chr6:1842800-1851000	Weak transcription	Pancreas	Pancrea
12	chr6:1842800-1872400	Weak transcription	Gastric	stomach
13	chr6:1845200-1847200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:1845600-1861200	Weak transcription	Aorta	Aorta
15	chr6:1845800-1846200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:1845800-1846200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:1845800-1846200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
18	chr6:1845800-1846400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:1845800-1846600	ZNF genes & repeats	Fetal Intestine Small	intestine
20	chr6:1845800-1847200	ZNF genes & repeats	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links