Variant report

Variant	rs1363839
Chromosome Location	chr5:90671274-90671275
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:90671164-90671594	H1-neurons	neurons:	n/a	n/a
2	REST	chr5:90670312-90680754	H1-neurons	neurons:	n/a	chr5:90679211-90679220 chr5:90679214-90679227 chr5:90676125-90676138 chr5:90676125-90676138
3	POLR2A	chr5:90662204-90681025	K562	blood:	n/a	n/a
4	REST	chr5:90671233-90674189	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr5:90671128-90671477	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr5:90661633-90680586	U87	brain:	n/a	n/a
7	POLR2A	chr5:90661706-90680586	U87	brain:	n/a	n/a
8	POLR2A	chr5:90662941-90671641	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr5:90670246-90671506	K562	blood:	n/a	n/a
10	POLR2A	chr5:90671248-90671493	HCT-116	colon:	n/a	n/a
11	POLR2A	chr5:90671056-90672093	K562	blood:	n/a	n/a
12	POLR2A	chr5:90661114-90672065	U87	brain:	n/a	n/a
13	POLR2A	chr5:90671250-90671506	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:90609791..90613058-chr5:90669226..90672505,3	MCF-7	breast:

Variant related genes	Relation type
ARRDC3	TF binding region
ENSG00000271762	Chromatin interaction
ENSG00000248323	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10041402	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10045280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10052492	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10054820	0.90[EUR][1000 genomes]
rs10058025	0.94[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes]
rs10059163	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10063683	0.94[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs10073657	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10073935	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1035476	0.89[EUR][1000 genomes]
rs1035477	0.90[EUR][1000 genomes]
rs10474352	0.86[CHB][hapmap];0.91[EUR][1000 genomes]
rs10474353	0.81[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10942634	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11948056	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11948075	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11950530	0.94[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs11955120	0.89[EUR][1000 genomes]
rs11959525	0.94[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.93[EUR][1000 genomes]
rs12110065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12110303	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12188467	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12651840	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12654787	0.94[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs12655973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12656350	0.90[EUR][1000 genomes]
rs1477348	0.93[EUR][1000 genomes]
rs1477349	0.93[EUR][1000 genomes]
rs186717	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1895448	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1895449	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1964292	0.88[EUR][1000 genomes]
rs1966494	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2004483	0.91[EUR][1000 genomes]
rs2052553	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2059207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2059208	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2367353	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2367526	0.88[EUR][1000 genomes]
rs2839728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2887007	0.88[EUR][1000 genomes]
rs332531	0.87[AMR][1000 genomes]
rs332544	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35712350	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4382199	0.90[EUR][1000 genomes]
rs60513756	0.91[EUR][1000 genomes]
rs6452951	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6452953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6452954	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66759971	0.89[EUR][1000 genomes]
rs6860948	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6865495	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6866191	0.90[EUR][1000 genomes]
rs6866923	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867091	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6869048	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6869717	0.93[EUR][1000 genomes]
rs6882269	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs746637	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7705465	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7708782	0.94[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes]
rs7715402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7718871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7720132	0.94[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs7720235	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs889213	0.94[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9293568	0.90[EUR][1000 genomes]
rs9686361	0.90[EUR][1000 genomes]
rs985434	0.94[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90662400-90673000	Strong transcription	Fetal Intestine Large	intestine
2	chr5:90662800-90672400	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr5:90663000-90671600	Strong transcription	Fetal Muscle Leg	muscle
4	chr5:90663000-90672400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr5:90663000-90672400	Strong transcription	Muscle Satellite Cultured Cells	--
6	chr5:90663000-90672800	Strong transcription	Adipose Nuclei	Adipose
7	chr5:90663000-90673400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:90663000-90673600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:90663000-90674200	Strong transcription	NH-A	brain
10	chr5:90663000-90674400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:90663000-90674400	Strong transcription	Placenta	Placenta
12	chr5:90663000-90674400	Strong transcription	Fetal Thymus	thymus
13	chr5:90663000-90674600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr5:90663200-90671400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr5:90663200-90671400	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr5:90663200-90671600	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr5:90663200-90672400	Strong transcription	Osteobl	bone
18	chr5:90663200-90672600	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr5:90663200-90673000	Strong transcription	Primary B cells from cord blood	blood
20	chr5:90663200-90673000	Strong transcription	Fetal Muscle Trunk	muscle
21	chr5:90663200-90673800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr5:90663200-90674000	Strong transcription	Duodenum Mucosa	Duodenum
23	chr5:90663400-90673200	Strong transcription	Primary hematopoietic stem cells	blood
24	chr5:90663400-90673800	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr5:90663400-90674000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:90663400-90674400	Strong transcription	Primary B cells from peripheral blood	blood
27	chr5:90663400-90674400	Strong transcription	HSMM	muscle
28	chr5:90663600-90672600	Strong transcription	HSMMtube	muscle
29	chr5:90663800-90673000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:90663800-90673000	Strong transcription	HMEC	breast
31	chr5:90663800-90673400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr5:90663800-90674200	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr5:90663800-90674400	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr5:90663800-90674400	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr5:90663800-90674600	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr5:90664000-90673600	Strong transcription	K562	blood
37	chr5:90664000-90673800	Strong transcription	Dnd41	blood
38	chr5:90664000-90673800	Strong transcription	GM12878-XiMat	blood
39	chr5:90664400-90671600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr5:90664600-90673800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr5:90665200-90671600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr5:90665200-90673200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr5:90665400-90673200	Strong transcription	NHEK	skin
44	chr5:90665400-90674000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr5:90665800-90673800	Strong transcription	HepG2	liver
46	chr5:90666200-90671400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
47	chr5:90666200-90672600	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr5:90667000-90672600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr5:90667200-90674800	Weak transcription	Aorta	Aorta
50	chr5:90667400-90673000	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links