Variant report

Variant	rs11962552
Chromosome Location	chr6:53595753-53595754
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:53587433..53591147-chr6:53595586..53599292,4	MCF-7	breast:
2	chr6:53593116..53596418-chr6:53657644..53660881,3	MCF-7	breast:
3	chr6:53595711..53597938-chr6:53598268..53600839,2	MCF-7	breast:
4	chr6:53592971..53596675-chr6:53657710..53661284,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228614	Chromatin interaction
ENSG00000137269	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10456165	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10456673	1.00[CEU][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10456674	0.82[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10948768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10948782	0.87[CHD][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap]
rs11968082	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12202762	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12204130	0.93[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12211417	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12211478	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12213577	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12216441	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13205690	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13211528	0.87[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34113003	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34876933	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35078422	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35143842	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35868455	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4373362	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4639324	0.87[CHD][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap]
rs67656923	0.81[ASN][1000 genomes]
rs72941941	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53589800-53599400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:53591000-53596800	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr6:53591000-53599000	Weak transcription	Stomach Mucosa	stomach
4	chr6:53591200-53596600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr6:53591200-53599600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr6:53591200-53599800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr6:53591600-53599600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:53592800-53596600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:53593000-53599800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:53593600-53595800	Weak transcription	Ovary	ovary
11	chr6:53593600-53596000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:53593600-53596200	Weak transcription	Fetal Thymus	thymus
13	chr6:53593600-53596600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:53593600-53596600	Weak transcription	Primary T cells from cord blood	blood
15	chr6:53593600-53596600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr6:53593600-53596600	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:53593600-53596800	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr6:53593600-53596800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:53593600-53596800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:53593600-53598400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:53593600-53598400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:53593600-53598600	Weak transcription	Fetal Intestine Large	intestine
23	chr6:53593600-53599000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr6:53593600-53599200	Weak transcription	NH-A	brain
25	chr6:53593600-53599400	Enhancers	Hela-S3	cervix
26	chr6:53593600-53599400	Weak transcription	HSMMtube	muscle
27	chr6:53593600-53599800	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr6:53593600-53600000	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr6:53593800-53596800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr6:53593800-53597200	Weak transcription	NHEK	skin
31	chr6:53593800-53598400	Weak transcription	Fetal Intestine Small	intestine
32	chr6:53593800-53598400	Weak transcription	HMEC	breast
33	chr6:53593800-53598600	Weak transcription	A549	lung
34	chr6:53593800-53599200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr6:53593800-53599800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:53594400-53596000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:53594600-53596000	Enhancers	Brain Germinal Matrix	brain
38	chr6:53594600-53599600	Weak transcription	Placenta	Placenta
39	chr6:53594800-53596000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr6:53594800-53596000	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr6:53594800-53596000	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr6:53595000-53595800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:53595000-53595800	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr6:53595000-53595800	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr6:53595000-53596000	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr6:53595000-53596000	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr6:53595000-53596000	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr6:53595000-53599800	Enhancers	Dnd41	blood
49	chr6:53595200-53595800	Enhancers	Fetal Brain Male	brain
50	chr6:53595200-53595800	Enhancers	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links