Variant report

Variant	rs584046
Chromosome Location	chr11:75341422-75341423
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:75324179..75326709-chr11:75339433..75341583,3	K562	blood:
2	chr11:75340982..75343512-chr11:75355129..75357190,2	K562	blood:
3	chr11:75332696..75337381-chr11:75337684..75342464,5	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1368135	1.00[ASW][hapmap];0.81[LWK][hapmap];0.83[AMR][1000 genomes]
rs2015782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2511005	0.81[CEU][hapmap];0.94[CHB][hapmap];0.84[EUR][1000 genomes]
rs544997	0.90[CEU][hapmap];0.94[CHB][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs570559	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs581522	0.83[EUR][1000 genomes]
rs585433	0.82[JPT][hapmap]
rs588955	0.82[JPT][hapmap]
rs589063	0.82[JPT][hapmap]
rs599816	0.82[JPT][hapmap]
rs601142	0.86[CEU][hapmap];0.94[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs601293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs609131	0.93[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs611221	0.86[CEU][hapmap];0.94[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs617449	0.94[CHB][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs61897968	0.85[AMR][1000 genomes]
rs629176	0.94[CHB][hapmap];0.83[EUR][1000 genomes]
rs636418	0.82[JPT][hapmap]
rs640277	0.81[EUR][1000 genomes]
rs642002	0.82[CEU][hapmap];0.94[CHB][hapmap];0.84[EUR][1000 genomes]
rs644388	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs648930	0.86[CEU][hapmap];0.94[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs652524	0.94[CHB][hapmap];0.81[EUR][1000 genomes]
rs664133	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs678320	0.82[EUR][1000 genomes]
rs678874	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs683195	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs684644	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][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	esv3381903	chr11:75123498-75587233	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs584046	GAB2	cis	parietal	SCAN
rs584046	C2CD3	cis	parietal	SCAN
rs584046	P2RY2	cis	cerebellum	SCAN
rs584046	SLCO2B1	cis	cerebellum	SCAN
rs584046	KRTAP5-9	cis	cerebellum	SCAN
rs584046	CTD-2530H12.4	cis	Artery Tibial	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75305800-75346200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr11:75317600-75346200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr11:75326800-75343600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:75330000-75350800	Weak transcription	Lung	lung
5	chr11:75330200-75356200	Weak transcription	Aorta	Aorta
6	chr11:75335400-75343000	Weak transcription	Fetal Intestine Small	intestine
7	chr11:75335400-75346800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr11:75336000-75343200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:75338000-75344000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr11:75338000-75346000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr11:75338600-75342200	Weak transcription	Fetal Brain Male	brain
12	chr11:75338600-75343400	Weak transcription	Fetal Brain Female	brain
13	chr11:75338800-75346400	Weak transcription	Brain Anterior Caudate	brain
14	chr11:75339000-75344800	Weak transcription	Fetal Heart	heart
15	chr11:75339000-75350400	Weak transcription	Brain Angular Gyrus	brain
16	chr11:75339200-75346400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr11:75339200-75346600	Weak transcription	Spleen	Spleen
18	chr11:75339400-75346200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr11:75339600-75344200	Weak transcription	Fetal Stomach	stomach
20	chr11:75339600-75344600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr11:75339600-75345600	Weak transcription	Ovary	ovary
22	chr11:75339800-75342400	Weak transcription	HSMMtube	muscle
23	chr11:75339800-75343800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr11:75339800-75344800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr11:75339800-75344800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr11:75340000-75344400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr11:75340000-75344400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr11:75340000-75344400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr11:75340000-75344600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr11:75340000-75344600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr11:75340000-75352600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr11:75340200-75341600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr11:75340200-75342400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:75340200-75342600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr11:75341000-75343600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:75341200-75342000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr11:75341200-75342800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr11:75341200-75344800	Weak transcription	Fetal Lung	lung
39	chr11:75341200-75345600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr11:75341400-75348200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links