Variant report

Variant	rs62308153
Chromosome Location	chr4:57783603-57783604
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57772971..57776902-chr4:57777481..57784789,10	MCF-7	breast:
2	chr4:57776711..57779494-chr4:57781932..57784622,2	MCF-7	breast:
3	chr4:57773013..57775637-chr4:57781437..57784341,3	MCF-7	breast:
4	chr4:57772930..57780141-chr4:57782916..57788353,10	K562	blood:

Variant related genes	Relation type
ENSG00000084093	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11721387	0.82[ASN][1000 genomes]
rs11726410	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11726443	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11726548	0.82[ASN][1000 genomes]
rs11727329	1.00[ASN][1000 genomes]
rs11730396	0.90[AMR][1000 genomes]
rs11731657	0.82[ASN][1000 genomes]
rs13123018	0.92[ASN][1000 genomes]
rs13125082	1.00[ASN][1000 genomes]
rs13128671	0.92[ASN][1000 genomes]
rs13130600	1.00[ASN][1000 genomes]
rs13130604	0.92[ASN][1000 genomes]
rs2412761	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34308849	0.91[ASN][1000 genomes]
rs34840470	0.91[ASN][1000 genomes]
rs34937594	0.91[ASN][1000 genomes]
rs35185186	0.92[ASN][1000 genomes]
rs35318869	0.91[ASN][1000 genomes]
rs4109037	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4413466	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4443350	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56143151	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56309796	0.82[EUR][1000 genomes]
rs62308068	0.82[ASN][1000 genomes]
rs62308099	0.91[ASN][1000 genomes]
rs62308100	0.91[ASN][1000 genomes]
rs62308107	0.91[ASN][1000 genomes]
rs66619445	0.92[ASN][1000 genomes]
rs6839166	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7684642	0.91[ASN][1000 genomes]
rs7685053	0.91[ASN][1000 genomes]
rs9055	0.92[ASN][1000 genomes]
rs9760540	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv3425352	chr4:57783591-57820951	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57775800-57786200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:57776400-57784000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr4:57776400-57789400	Weak transcription	Right Ventricle	heart
4	chr4:57777000-57784400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:57777000-57785400	Genic enhancers	Primary T cells fromperipheralblood	blood
6	chr4:57777000-57786400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:57777000-57795800	Weak transcription	A549	lung
8	chr4:57777000-57796600	Weak transcription	Fetal Brain Female	brain
9	chr4:57777000-57797000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr4:57777200-57793400	Weak transcription	HMEC	breast
11	chr4:57777200-57796600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:57777200-57796600	Weak transcription	Aorta	Aorta
13	chr4:57777200-57796800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:57777200-57797200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr4:57777400-57784600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:57777400-57786200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr4:57777600-57784000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
18	chr4:57777600-57785800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr4:57777600-57796000	Weak transcription	Brain Anterior Caudate	brain
20	chr4:57777600-57796000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr4:57777600-57796600	Weak transcription	Colonic Mucosa	Colon
22	chr4:57777600-57803200	Weak transcription	NHDF-Ad	bronchial
23	chr4:57777600-57805600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:57777600-57806000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr4:57778000-57785600	Strong transcription	Fetal Stomach	stomach
26	chr4:57778000-57791800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:57778000-57796000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr4:57778000-57796000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr4:57778000-57796600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr4:57778000-57797000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr4:57778200-57784000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr4:57778200-57784000	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr4:57778200-57784200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:57778200-57785600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr4:57778200-57796200	Weak transcription	Brain Hippocampus Middle	brain
36	chr4:57778200-57796800	Weak transcription	NHLF	lung
37	chr4:57778400-57784400	Weak transcription	NH-A	brain
38	chr4:57778400-57786200	Weak transcription	HSMM	muscle
39	chr4:57778400-57788600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:57778400-57795400	Weak transcription	HSMMtube	muscle
41	chr4:57778400-57796000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr4:57778400-57800200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr4:57778400-57800200	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr4:57778400-57801000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:57778600-57785200	Strong transcription	Fetal Intestine Small	intestine
46	chr4:57778800-57795800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr4:57779000-57804600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr4:57779200-57799200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr4:57779400-57785000	Weak transcription	Lung	lung
50	chr4:57779800-57784200	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links