Variant report

Variant	rs11969398
Chromosome Location	chr6:1858071-1858072
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: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11963926	0.81[AFR][1000 genomes]
rs11967089	0.81[AFR][1000 genomes]
rs11968685	0.81[AFR][1000 genomes]
rs11969147	0.85[AFR][1000 genomes]
rs17134424	0.85[AFR][1000 genomes]
rs17134428	0.85[AFR][1000 genomes]
rs7758701	0.85[AFR][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:35 , 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	chr6:1855800-1866200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:1856800-1860200	Strong transcription	HepG2	liver
11	chr6:1856800-1869600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:1857000-1861600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:1857000-1862200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:1857000-1862400	Weak transcription	NHEK	skin
15	chr6:1857000-1864600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr6:1857000-1864800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr6:1857000-1864800	Weak transcription	Ovary	ovary
18	chr6:1857200-1858600	Enhancers	Dnd41	blood
19	chr6:1857200-1858800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr6:1857200-1861000	Weak transcription	Primary B cells from cord blood	blood
21	chr6:1857200-1861600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:1857200-1863800	Weak transcription	Fetal Intestine Small	intestine
23	chr6:1857200-1866200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:1857400-1858400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr6:1857400-1859200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:1857600-1859400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:1857600-1866000	Weak transcription	Left Ventricle	heart
28	chr6:1857600-1877200	Weak transcription	Primary T cells from cord blood	blood
29	chr6:1857800-1858600	Weak transcription	Brain Germinal Matrix	brain
30	chr6:1857800-1858800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr6:1857800-1859200	Weak transcription	Fetal Muscle Leg	muscle
32	chr6:1857800-1860200	Weak transcription	Right Atrium	heart
33	chr6:1857800-1860800	Weak transcription	GM12878-XiMat	blood
34	chr6:1857800-1861000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr6:1858000-1858800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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