Variant report

Variant	rs2281760
Chromosome Location	chr6:1866526-1866527
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:1860563..1862869-chr6:1864416..1866746,2	K562	blood:
2	chr6:1858177..1860635-chr6:1865077..1867804,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10900914	0.84[JPT][hapmap]
rs11969985	0.86[JPT][hapmap]
rs12664587	0.86[JPT][hapmap]
rs1467594	1.00[CEU][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1543538	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1570533	0.82[CEU][hapmap];0.82[TSI][hapmap]
rs1570535	0.84[ASW][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2296131	0.92[CEU][hapmap];0.82[YRI][hapmap];0.92[EUR][1000 genomes]
rs2628442	0.86[JPT][hapmap]
rs2628445	0.86[JPT][hapmap]
rs2761233	0.86[JPT][hapmap]
rs3778537	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs3778538	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3778540	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs3800091	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs3800097	0.92[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.85[LWK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3800099	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs3800100	0.84[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.98[EUR][1000 genomes]
rs3800102	0.95[CEU][hapmap]
rs3800103	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs3800104	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs3800106	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs3800107	0.96[CEU][hapmap];0.87[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3800108	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs3800115	0.92[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs3800121	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3800122	0.82[CEU][hapmap];0.84[TSI][hapmap]
rs3800136	0.86[JPT][hapmap]
rs3823277	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs4959160	0.84[ASW][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs6940806	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7759192	0.86[JPT][hapmap]
rs7759496	0.86[JPT][hapmap]
rs912310	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9328073	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs9378661	1.00[ASW][hapmap];0.89[CEU][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9391935	0.94[EUR][1000 genomes]
rs9392341	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9392342	0.89[CEU][hapmap]
rs9405152	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9405521	0.82[EUR][1000 genomes]
rs9405522	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
12	nsv1032149	chr6:1848148-2006021	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1842800-1872400	Weak transcription	Gastric	stomach
2	chr6:1851200-1895600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:1851400-1872200	Weak transcription	Pancreas	Pancrea
4	chr6:1851400-1909600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:1856800-1869600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:1857600-1877200	Weak transcription	Primary T cells from cord blood	blood
7	chr6:1861400-1870400	Weak transcription	Colonic Mucosa	Colon
8	chr6:1861600-1870000	Weak transcription	Aorta	Aorta
9	chr6:1862800-1868000	Weak transcription	GM12878-XiMat	blood
10	chr6:1864400-1866600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:1864600-1866800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr6:1864600-1867000	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr6:1864600-1867200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:1864800-1866800	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr6:1864800-1866800	Enhancers	Fetal Kidney	kidney
16	chr6:1864800-1867200	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr6:1864800-1867400	Enhancers	HepG2	liver
18	chr6:1865000-1866800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr6:1865200-1869600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr6:1865200-1884600	Weak transcription	Small Intestine	intestine
21	chr6:1865400-1866600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:1865400-1869400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr6:1865400-1869600	Weak transcription	Ovary	ovary
24	chr6:1865400-1870600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr6:1865400-1871000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:1865600-1867200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:1865600-1869200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr6:1865800-1867000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:1865800-1870200	Weak transcription	Brain Anterior Caudate	brain
30	chr6:1865800-1872200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:1866000-1867200	Enhancers	H1 Cell Line	embryonic stem cell
32	chr6:1866000-1867200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:1866000-1868000	Enhancers	Stomach Mucosa	stomach
34	chr6:1866000-1869600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:1866200-1866600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:1866200-1867000	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr6:1866200-1867000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr6:1866400-1867000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr6:1866400-1869200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr6:1866400-1870000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr6:1866400-1870600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:1866400-1871600	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links