Variant report

Variant	rs11588643
Chromosome Location	chr1:76255613-76255614
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:35)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:35 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:76249993-76263987	K562	blood:	n/a	n/a
2	NFATC1	chr1:76254451-76255808	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:76255418-76255849	HepG2	liver:	n/a	n/a
4	IRF1	chr1:76255100-76255919	K562	blood:	n/a	n/a
5	POLR2A	chr1:76250010-76263479	K562	blood:	n/a	n/a
6	POLR2A	chr1:76255507-76256178	K562	blood:	n/a	n/a
7	POLR2A	chr1:76250991-76264029	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr1:76250033-76264125	K562	blood:	n/a	n/a
9	POLR2A	chr1:76251073-76257428	HepG2	liver:	n/a	n/a
10	POLR2A	chr1:76251198-76257365	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr1:76251042-76257307	U87	brain:	n/a	n/a
12	POLR2A	chr1:76255535-76256020	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr1:76250068-76266595	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:76251108-76257452	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr1:76255480-76256281	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr1:76254319-76256182	HepG2	liver:	n/a	n/a
17	POLR2A	chr1:76255535-76255965	HepG2	liver:	n/a	n/a
18	POLR2A	chr1:76250047-76263901	GM18505	blood:	n/a	n/a
19	POLR2A	chr1:76249945-76266639	GM12891	blood:	n/a	n/a
20	POLR2A	chr1:76250036-76264085	K562	blood:	n/a	n/a
21	POLR2A	chr1:76250200-76257400	GM19099	blood:	n/a	n/a
22	POLR2A	chr1:76255510-76257063	SK-N-MC	brain:	n/a	n/a
23	POLR2A	chr1:76250996-76257615	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr1:76251203-76256991	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr1:76250185-76257476	GM12892	blood:	n/a	n/a
26	POLR2A	chr1:76251241-76256430	U87	brain:	n/a	n/a
27	POLR2A	chr1:76255239-76255741	K562	blood:	n/a	n/a
28	POLR2A	chr1:76252995-76255924	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr1:76251219-76256431	U87	brain:	n/a	n/a
30	POLR2A	chr1:76250012-76264059	K562	blood:	n/a	n/a
31	POLR2A	chr1:76250199-76255744	HCT-116	colon:	n/a	n/a
32	POLR2A	chr1:76255550-76256191	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr1:76254458-76256363	GM12878	blood:	n/a	n/a
34	POLR2A	chr1:76251020-76258361	U87	brain:	n/a	n/a
35	CHD1	chr1:76255510-76255891	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:76186306..76195796-chr1:76248732..76266552,73	K562	blood:
2	chr1:76187424..76195796-chr1:76248839..76258922,52	K562	blood:
3	chr1:76195849..76201919-chr1:76251987..76255873,8	K562	blood:
4	chr1:76197028..76199654-chr1:76253368..76256114,2	K562	blood:
5	chr1:76213598..76215985-chr1:76254500..76257122,2	K562	blood:

No data

Variant related genes	Relation type
RABGGTB	TF binding region
ENSG00000178193	Chromatin interaction
ENSG00000117054	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1001160	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap]
rs10873797	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap]
rs11161699	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161848	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap]
rs11161887	0.84[CEU][hapmap]
rs11161902	1.00[JPT][hapmap]
rs11163967	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11164042	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1146631	1.00[JPT][hapmap]
rs1146634	1.00[JPT][hapmap]
rs1146636	1.00[JPT][hapmap]
rs1146644	1.00[JPT][hapmap]
rs11578480	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11579752	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11584577	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1159215	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs11810154	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12043473	1.00[JPT][hapmap]
rs12118229	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12118306	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12130832	0.95[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12131344	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs12132750	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12138018	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12142247	0.95[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12145870	0.84[EUR][1000 genomes]
rs1250876	0.84[CEU][hapmap]
rs1250880	0.81[CEU][hapmap]
rs1303870	0.84[CEU][hapmap]
rs1463812	1.00[JPT][hapmap]
rs1498311	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1628063	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap]
rs1630587	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1689270	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17647178	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17647711	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1770889	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17848068	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1796813	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1796815	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1796827	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1846233	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs1856791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1908089	0.84[CEU][hapmap]
rs2029682	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4403585	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4638068	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4646960	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5745323	1.00[JPT][hapmap]
rs5745325	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745347	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5745430	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5745523	0.84[CEU][hapmap]
rs5745543	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs5745545	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs5745546	0.84[CEU][hapmap]
rs5745547	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs60550898	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6593520	1.00[JPT][hapmap]
rs6593521	1.00[JPT][hapmap]
rs6656501	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664254	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6675212	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6704444	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs721204	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs72979226	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74090722	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74090730	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7516477	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11588643	SNORD45B	cis	cerebellum	SCAN
rs11588643	RABGGTB	cis	cerebellum	SCAN
rs11588643	SNORD45B	cis	parietal	SCAN
rs11588643	TFDP2	trans	lymphoblastoid	seeQTL
rs11588643	PIGK	cis	parietal	SCAN
rs11588643	FAM73A	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76251200-76256200	Active TSS	Right Ventricle	heart
2	chr1:76252200-76258400	Weak transcription	Spleen	Spleen
3	chr1:76252400-76258800	Transcr. at gene 5' and 3'	K562	blood
4	chr1:76252600-76257600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:76252800-76256000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
6	chr1:76252800-76256800	Transcr. at gene 5' and 3'	Dnd41	blood
7	chr1:76252800-76257000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
8	chr1:76252800-76257000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:76252800-76257200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
10	chr1:76253000-76255800	Transcr. at gene 5' and 3'	HMEC	breast
11	chr1:76253000-76256000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
12	chr1:76253000-76256800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
13	chr1:76253000-76257400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
14	chr1:76253200-76256000	Transcr. at gene 5' and 3'	NH-A	brain
15	chr1:76253200-76256600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:76253200-76256600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:76253200-76257400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:76253400-76256800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:76253600-76255800	Enhancers	Brain Substantia Nigra	brain
20	chr1:76253600-76256200	Weak transcription	Esophagus	oesophagus
21	chr1:76253600-76256800	Genic enhancers	Primary monocytes fromperipheralblood	blood
22	chr1:76253600-76257400	Transcr. at gene 5' and 3'	Hela-S3	cervix
23	chr1:76253800-76257000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
24	chr1:76254000-76255800	Transcr. at gene 5' and 3'	Psoas Muscle	Psoas
25	chr1:76254000-76256600	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:76254000-76257000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:76254000-76260000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr1:76254200-76255800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:76254200-76255800	Enhancers	Brain Cingulate Gyrus	brain
30	chr1:76254200-76256000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:76254200-76256200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:76254200-76256200	Weak transcription	Lung	lung
33	chr1:76254200-76257400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr1:76254200-76258400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:76254200-76258600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
36	chr1:76254200-76263200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:76254400-76255800	Weak transcription	Fetal Muscle Leg	muscle
38	chr1:76254400-76255800	Weak transcription	Gastric	stomach
39	chr1:76254400-76255800	Weak transcription	Left Ventricle	heart
40	chr1:76254400-76255800	Weak transcription	Small Intestine	intestine
41	chr1:76254400-76256000	Weak transcription	Fetal Stomach	stomach
42	chr1:76254400-76256400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:76254400-76256400	Weak transcription	Pancreas	Pancrea
44	chr1:76254400-76256600	Genic enhancers	Primary B cells from peripheral blood	blood
45	chr1:76254400-76256600	Genic enhancers	Adipose Nuclei	Adipose
46	chr1:76254400-76256800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
47	chr1:76254400-76257400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
48	chr1:76254400-76262400	Strong transcription	Placenta	Placenta
49	chr1:76254400-76265200	Strong transcription	Fetal Muscle Trunk	muscle
50	chr1:76254600-76255800	Transcr. at gene 5' and 3'	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links