Variant report

Variant	rs9474640
Chromosome Location	chr6:53593855-53593856
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:53375847..53377727-chr6:53591880..53594689,2	MCF-7	breast:
2	chr6:53593116..53596418-chr6:53657644..53660881,3	MCF-7	breast:
3	chr6:53357447..53358709-chr6:53592427..53594072,11	K562	blood:
4	chr6:53589302..53590903-chr6:53592714..53595336,2	K562	blood:
5	chr6:53592971..53596675-chr6:53657710..53661284,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137269	Chromatin interaction
ENSG00000228614	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10456672	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11751003	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11758147	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13216331	0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4295480	0.81[AMR][1000 genomes]
rs4345397	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4373352	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4400206	0.95[CEU][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4404762	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4441952	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4457161	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4516937	0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4563705	0.94[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4610551	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4712043	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4712044	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4715418	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6908232	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6921605	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6925356	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6934324	0.95[CHB][hapmap];0.85[JPT][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7749273	0.95[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7756512	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7763482	0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7773852	0.86[CHB][hapmap]
rs7774024	0.87[CHB][hapmap];0.80[AMR][1000 genomes]
rs7776124	0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9382235	0.88[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9474639	0.95[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9474641	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9474646	0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9474649	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[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:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53588800-53594600	Enhancers	Placenta	Placenta
2	chr6:53589400-53594400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:53589800-53594800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:53589800-53595000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:53589800-53595000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr6:53589800-53599400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:53590000-53595000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr6:53590200-53595000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:53591000-53596800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr6:53591000-53599000	Weak transcription	Stomach Mucosa	stomach
11	chr6:53591200-53595000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:53591200-53596600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:53591200-53599600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr6:53591200-53599800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr6:53591600-53599600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:53592800-53596600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:53593000-53599800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:53593600-53594600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr6:53593600-53594800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:53593600-53595000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:53593600-53595800	Weak transcription	Ovary	ovary
22	chr6:53593600-53596000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:53593600-53596200	Weak transcription	Fetal Thymus	thymus
24	chr6:53593600-53596600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:53593600-53596600	Weak transcription	Primary T cells from cord blood	blood
26	chr6:53593600-53596600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr6:53593600-53596600	Weak transcription	Fetal Muscle Leg	muscle
28	chr6:53593600-53596800	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr6:53593600-53596800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:53593600-53596800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:53593600-53598400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:53593600-53598400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:53593600-53598600	Weak transcription	Fetal Intestine Large	intestine
34	chr6:53593600-53599000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr6:53593600-53599200	Weak transcription	NH-A	brain
36	chr6:53593600-53599400	Enhancers	Hela-S3	cervix
37	chr6:53593600-53599400	Weak transcription	HSMMtube	muscle
38	chr6:53593600-53599800	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr6:53593600-53600000	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr6:53593800-53595000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr6:53593800-53595000	Weak transcription	Dnd41	blood
42	chr6:53593800-53595200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr6:53593800-53596800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:53593800-53597200	Weak transcription	NHEK	skin
45	chr6:53593800-53598400	Weak transcription	Fetal Intestine Small	intestine
46	chr6:53593800-53598400	Weak transcription	HMEC	breast
47	chr6:53593800-53598600	Weak transcription	A549	lung
48	chr6:53593800-53599200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr6:53593800-53599800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links