Variant report

Variant	rs12364988
Chromosome Location	chr11:121367626-121367627
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12798073	0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs2009383	0.88[EUR][1000 genomes]
rs3862606	0.94[JPT][hapmap]
rs4631890	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs523917	0.80[EUR][1000 genomes]
rs596437	0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs599161	0.82[EUR][1000 genomes]
rs633197	0.80[EUR][1000 genomes]
rs641120	0.80[EUR][1000 genomes]
rs656338	0.81[EUR][1000 genomes]
rs668387	0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs687228	0.81[EUR][1000 genomes]
rs689021	0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs923892	0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs923893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv898427	chr11:121299288-121411041	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	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
3	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12364988	BCL9L	cis	cerebellum	SCAN
rs12364988	C2CD2L	cis	parietal	SCAN
rs12364988	CD3G	cis	cerebellum	SCAN
rs12364988	SIK3	cis	cerebellum	SCAN
rs12364988	MLL	cis	cerebellum	SCAN
rs12364988	TMEM25	cis	cerebellum	SCAN
rs12364988	HEPACAM	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:121349800-121393000	Weak transcription	Colonic Mucosa	Colon
2	chr11:121350000-121401400	Weak transcription	Fetal Brain Male	brain
3	chr11:121350200-121367800	Weak transcription	Fetal Kidney	kidney
4	chr11:121350400-121393200	Weak transcription	Gastric	stomach
5	chr11:121350800-121368400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr11:121351400-121384600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr11:121352800-121377600	Strong transcription	HepG2	liver
8	chr11:121353600-121377000	Weak transcription	Pancreas	Pancrea
9	chr11:121353800-121374200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:121359000-121367800	Weak transcription	Brain Substantia Nigra	brain
11	chr11:121359200-121367800	Weak transcription	Aorta	Aorta
12	chr11:121359200-121369800	Weak transcription	Left Ventricle	heart
13	chr11:121359200-121384200	Weak transcription	Fetal Stomach	stomach
14	chr11:121359600-121367800	Weak transcription	Spleen	Spleen
15	chr11:121359800-121377000	Weak transcription	Esophagus	oesophagus
16	chr11:121360600-121368400	Weak transcription	Brain Germinal Matrix	brain
17	chr11:121360800-121369800	Weak transcription	Brain Hippocampus Middle	brain
18	chr11:121360800-121384400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr11:121362800-121367800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr11:121362800-121368000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr11:121364000-121375800	Strong transcription	Liver	Liver
22	chr11:121365000-121371200	Strong transcription	Fetal Intestine Large	intestine
23	chr11:121365000-121371200	Strong transcription	Fetal Intestine Small	intestine
24	chr11:121365800-121368000	Weak transcription	HMEC	breast
25	chr11:121365800-121371200	Weak transcription	Fetal Muscle Leg	muscle
26	chr11:121365800-121372200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr11:121365800-121374000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr11:121365800-121374600	Strong transcription	Dnd41	blood
29	chr11:121365800-121377200	Weak transcription	Small Intestine	intestine
30	chr11:121365800-121392600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr11:121366000-121368000	Genic enhancers	Primary T cells fromperipheralblood	blood
32	chr11:121366000-121368400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr11:121366000-121369200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr11:121366000-121373600	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr11:121366000-121374200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr11:121366000-121374600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr11:121366200-121367800	Genic enhancers	Primary B cells from cord blood	blood
38	chr11:121366200-121367800	Weak transcription	Brain Angular Gyrus	brain
39	chr11:121366200-121368000	Weak transcription	Stomach Mucosa	stomach
40	chr11:121366200-121372800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr11:121366200-121373200	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr11:121366200-121373400	Strong transcription	Fetal Thymus	thymus
43	chr11:121366200-121373600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr11:121366400-121368000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr11:121366400-121368600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr11:121366400-121369000	Genic enhancers	HUES48 Cell Line	embryonic stem cell
47	chr11:121366400-121371200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr11:121366400-121375200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr11:121366400-121376400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr11:121366600-121367800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood

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