Variant report

Variant	rs56379320
Chromosome Location	chr1:62494455-62494456
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62488087..62490869-chr1:62492445..62494953,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10493313	0.87[EUR][1000 genomes]
rs11576777	0.85[EUR][1000 genomes]
rs11577828	0.93[ASN][1000 genomes]
rs11579010	0.87[EUR][1000 genomes]
rs11581307	0.93[ASN][1000 genomes]
rs11585888	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11587128	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11590485	0.93[ASN][1000 genomes]
rs11590812	0.93[ASN][1000 genomes]
rs11590954	0.93[ASN][1000 genomes]
rs1363	0.93[ASN][1000 genomes]
rs1412620	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17378995	0.91[EUR][1000 genomes]
rs2067881	0.87[ASN][1000 genomes]
rs2476180	0.93[ASN][1000 genomes]
rs4325166	0.93[ASN][1000 genomes]
rs4915603	0.93[ASN][1000 genomes]
rs4915795	0.93[ASN][1000 genomes]
rs61777665	0.93[ASN][1000 genomes]
rs61777666	0.93[ASN][1000 genomes]
rs6661849	0.92[EUR][1000 genomes]
rs6673889	0.92[EUR][1000 genomes]
rs6685356	0.92[EUR][1000 genomes]
rs6685442	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7519802	0.92[EUR][1000 genomes]
rs7528431	0.93[ASN][1000 genomes]
rs7531027	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539653	0.92[EUR][1000 genomes]
rs7556298	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518627	chr1:62279594-62517947	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv522020	chr1:62279594-62517947	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv531876	chr1:62302313-62504349	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
7	nsv945803	chr1:62490443-62495121	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62409200-62518600	Weak transcription	Pancreas	Pancrea
2	chr1:62458800-62521400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:62459000-62516000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:62459000-62530600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr1:62459200-62511200	Weak transcription	Gastric	stomach
6	chr1:62459200-62550000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:62460000-62499600	Weak transcription	Fetal Intestine Large	intestine
8	chr1:62460000-62516400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:62460000-62544600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:62460200-62516000	Weak transcription	HMEC	breast
11	chr1:62469000-62533600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:62474200-62518600	Weak transcription	Primary T cells from cord blood	blood
13	chr1:62479400-62496000	Weak transcription	Fetal Kidney	kidney
14	chr1:62480600-62513000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr1:62484400-62523000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:62484400-62562200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:62484600-62506000	Weak transcription	NHEK	skin
18	chr1:62484800-62511200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:62486200-62517600	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:62488000-62498000	Weak transcription	Fetal Heart	heart
21	chr1:62488400-62494600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:62488400-62494600	Weak transcription	Brain Germinal Matrix	brain
23	chr1:62488400-62497600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:62488400-62497600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:62488400-62521200	Weak transcription	Ovary	ovary
26	chr1:62488600-62499000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:62490600-62499200	Weak transcription	Right Atrium	heart
28	chr1:62491800-62499200	Weak transcription	Left Ventricle	heart
29	chr1:62491800-62511200	Weak transcription	Psoas Muscle	Psoas
30	chr1:62492400-62496200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:62493800-62494600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:62494000-62494600	ZNF genes & repeats	Fetal Intestine Small	intestine
33	chr1:62494000-62494800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:62494200-62494600	ZNF genes & repeats	Aorta	Aorta
35	chr1:62494200-62494600	ZNF genes & repeats	Esophagus	oesophagus
36	chr1:62494200-62494800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
37	chr1:62494200-62495000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
38	chr1:62494200-62495000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
39	chr1:62494200-62495000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
40	chr1:62494200-62495200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:62494400-62494800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
42	chr1:62494400-62494800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:62494400-62494800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:62494400-62495000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
45	chr1:62494400-62495200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:62494400-62495200	ZNF genes & repeats	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links