Variant report

Variant	rs3800099
Chromosome Location	chr6:1856960-1856961
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:1856826..1858830-chr6:1861067..1863033,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1467594	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1543538	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1570533	0.82[CEU][hapmap];0.82[TSI][hapmap]
rs2281760	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2296131	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs3778537	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs3778538	0.94[EUR][1000 genomes]
rs3778540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3800091	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs3800097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3800102	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs3800103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3800104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3800106	0.88[CEU][hapmap];0.95[MEX][hapmap];0.83[EUR][1000 genomes]
rs3800107	0.96[CEU][hapmap];0.99[EUR][1000 genomes]
rs3800108	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs3800115	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs3800121	0.89[CEU][hapmap]
rs3800122	0.82[CEU][hapmap];0.84[TSI][hapmap]
rs3823277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6940806	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9328073	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9378661	0.89[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs9391935	0.94[EUR][1000 genomes]
rs9392341	0.81[EUR][1000 genomes]
rs9392342	0.89[CEU][hapmap]
rs9405152	0.87[EUR][1000 genomes]
rs9405521	0.82[EUR][1000 genomes]
rs9405522	0.81[EUR][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:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1838200-1862200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:1842800-1872400	Weak transcription	Gastric	stomach
3	chr6:1845600-1861200	Weak transcription	Aorta	Aorta
4	chr6:1851200-1895600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:1851400-1861200	Weak transcription	Colonic Mucosa	Colon
6	chr6:1851400-1865000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:1851400-1872200	Weak transcription	Pancreas	Pancrea
8	chr6:1851400-1909600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:1853800-1857800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr6:1854800-1857800	Enhancers	Brain Germinal Matrix	brain
11	chr6:1855200-1857200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr6:1855800-1866200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:1856000-1857200	Flanking Active TSS	Dnd41	blood
14	chr6:1856200-1857000	Enhancers	H9 Cell Line	embryonic stem cell
15	chr6:1856200-1857000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:1856200-1857000	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr6:1856200-1857000	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr6:1856200-1857000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:1856200-1857000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:1856200-1857000	Enhancers	Brain Anterior Caudate	brain
21	chr6:1856200-1857000	Enhancers	Fetal Kidney	kidney
22	chr6:1856200-1857000	Flanking Active TSS	GM12878-XiMat	blood
23	chr6:1856200-1857200	Enhancers	H1 Cell Line	embryonic stem cell
24	chr6:1856200-1857200	Enhancers	Fetal Intestine Large	intestine
25	chr6:1856200-1857400	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr6:1856200-1857800	Enhancers	Primary B cells from peripheral blood	blood
27	chr6:1856200-1857800	Enhancers	Fetal Muscle Leg	muscle
28	chr6:1856400-1857000	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr6:1856400-1857000	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr6:1856400-1857000	Enhancers	Brain Cingulate Gyrus	brain
31	chr6:1856400-1857200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr6:1856400-1857200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr6:1856400-1857800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:1856600-1857000	Enhancers	Adipose Nuclei	Adipose
35	chr6:1856600-1857000	Enhancers	Brain Hippocampus Middle	brain
36	chr6:1856600-1857000	Enhancers	NHEK	skin
37	chr6:1856600-1857200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr6:1856600-1857600	Strong transcription	Primary T cells from cord blood	blood
39	chr6:1856800-1857000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:1856800-1857000	Enhancers	Ovary	ovary
41	chr6:1856800-1857200	Enhancers	Primary B cells from cord blood	blood
42	chr6:1856800-1857200	Enhancers	Fetal Intestine Small	intestine
43	chr6:1856800-1857600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:1856800-1860200	Strong transcription	HepG2	liver
45	chr6:1856800-1869600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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