Variant report

Variant	rs2276346
Chromosome Location	chr11:121414476-121414477
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:121410810..121412961-chr11:121413789..121415504,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10502262	0.82[MKK][hapmap]
rs10892752	1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.87[ASN][1000 genomes]
rs11218301	0.90[CHB][hapmap]
rs11218312	0.87[ASN][1000 genomes]
rs11218319	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs11218325	0.88[CEU][hapmap]
rs11218326	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11218335	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11512476	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs11518396	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs12360983	0.87[ASN][1000 genomes]
rs12361125	0.83[ASN][1000 genomes]
rs12795657	0.87[ASN][1000 genomes]
rs12796201	0.87[ASN][1000 genomes]
rs2009383	0.83[ASN][1000 genomes]
rs3933403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4935775	1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.87[ASN][1000 genomes]
rs7103597	0.88[CEU][hapmap]
rs7105365	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs7109029	0.87[ASN][1000 genomes]
rs7481208	0.87[ASN][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	nsv522474	chr11:121356968-121436270	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv975233	chr11:121359656-121574786	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2276346	ARHGEF12	cis	cerebellum	SCAN
rs2276346	VWA5A	cis	parietal	SCAN
rs2276346	USP2	cis	cerebellum	SCAN
rs2276346	C2CD2L	cis	cerebellum	SCAN
rs2276346	OR8B8	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:121385600-121418200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr11:121391400-121437200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:121392400-121414800	Weak transcription	Stomach Mucosa	stomach
4	chr11:121393600-121415400	Weak transcription	Colonic Mucosa	Colon
5	chr11:121395200-121434800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr11:121395400-121424600	Weak transcription	Gastric	stomach
7	chr11:121396400-121445000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr11:121396600-121437600	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr11:121396800-121415400	Weak transcription	Fetal Stomach	stomach
10	chr11:121396800-121417400	Weak transcription	Aorta	Aorta
11	chr11:121396800-121425400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:121397000-121434800	Weak transcription	Fetal Kidney	kidney
13	chr11:121399000-121443200	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr11:121404600-121437200	Weak transcription	Lung	lung
15	chr11:121404800-121417400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr11:121405400-121421000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr11:121405600-121437400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr11:121405800-121420800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:121406200-121417400	Weak transcription	Brain Angular Gyrus	brain
20	chr11:121406200-121423400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr11:121407200-121459000	Weak transcription	Colon Smooth Muscle	Colon
22	chr11:121408800-121416800	Weak transcription	Fetal Brain Female	brain
23	chr11:121409200-121415000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr11:121409800-121420800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr11:121409800-121423800	Strong transcription	Liver	Liver
26	chr11:121410000-121424600	Weak transcription	Ovary	ovary
27	chr11:121411400-121417000	Weak transcription	Brain Germinal Matrix	brain
28	chr11:121411400-121419000	Strong transcription	HepG2	liver
29	chr11:121411800-121433600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:121412200-121414800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr11:121412200-121420200	Weak transcription	HMEC	breast
32	chr11:121412400-121415000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr11:121412400-121419000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr11:121412800-121435200	Weak transcription	Small Intestine	intestine
35	chr11:121413600-121416200	Enhancers	Fetal Brain Male	brain
36	chr11:121413600-121429400	Weak transcription	Left Ventricle	heart
37	chr11:121414000-121415000	Strong transcription	Primary T cells from cord blood	blood
38	chr11:121414000-121415200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
39	chr11:121414000-121415400	Strong transcription	Esophagus	oesophagus
40	chr11:121414000-121416400	Genic enhancers	Primary B cells from peripheral blood	blood
41	chr11:121414000-121416400	Strong transcription	Fetal Intestine Small	intestine
42	chr11:121414000-121416600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:121414000-121416800	Strong transcription	Rectal Smooth Muscle	rectum
44	chr11:121414000-121417200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr11:121414000-121417600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
46	chr11:121414000-121417800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr11:121414000-121418400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:121414000-121418600	Genic enhancers	Primary T cells fromperipheralblood	blood
49	chr11:121414000-121418600	Strong transcription	Fetal Intestine Large	intestine
50	chr11:121414000-121418600	Strong transcription	Rectal Mucosa Donor 31	rectum

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