Variant report

Variant	rs4935775
Chromosome Location	chr11:121389502-121389503
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10892752	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11218301	0.89[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap]
rs11218312	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11218319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11218326	1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[ASN][1000 genomes]
rs11218335	0.83[ASN][1000 genomes]
rs11512476	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11518396	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12360983	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12361125	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12795657	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12796201	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2009383	0.96[ASN][1000 genomes]
rs2276346	1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.87[ASN][1000 genomes]
rs3933403	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs7105365	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7109029	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7481208	0.90[AMR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4935775	HEPACAM	cis	cerebellum	SCAN
rs4935775	CD3G	cis	cerebellum	SCAN
rs4935775	BCL9L	cis	cerebellum	SCAN
rs4935775	SIK3	cis	cerebellum	SCAN

Chromatin state (count:90 , 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	chr11:121350400-121393200	Weak transcription	Gastric	stomach
4	chr11:121365800-121392600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:121368400-121395800	Weak transcription	Fetal Kidney	kidney
6	chr11:121369000-121396800	Weak transcription	Ovary	ovary
7	chr11:121369400-121391000	Weak transcription	Colon Smooth Muscle	Colon
8	chr11:121375200-121390200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr11:121375400-121391000	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr11:121377000-121390400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr11:121377400-121390800	Weak transcription	HMEC	breast
12	chr11:121377400-121394400	Weak transcription	Pancreas	Pancrea
13	chr11:121377400-121396400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:121378000-121395800	Strong transcription	Primary T cells from cord blood	blood
15	chr11:121378400-121397800	Strong transcription	HepG2	liver
16	chr11:121379200-121391200	Strong transcription	Primary B cells from cord blood	blood
17	chr11:121379200-121392200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr11:121379200-121395800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr11:121379400-121389600	Strong transcription	Dnd41	blood
20	chr11:121379400-121390400	Strong transcription	GM12878-XiMat	blood
21	chr11:121379400-121395800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr11:121379400-121398000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr11:121380000-121395600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr11:121381000-121392000	Weak transcription	Stomach Mucosa	stomach
25	chr11:121381000-121397000	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr11:121381600-121391600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr11:121381600-121394400	Weak transcription	Lung	lung
28	chr11:121382800-121396600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr11:121383000-121398800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr11:121383600-121389600	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr11:121383800-121389600	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr11:121383800-121390400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr11:121384000-121394400	Weak transcription	Aorta	Aorta
34	chr11:121384000-121396200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr11:121384200-121393200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr11:121384600-121390800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr11:121385000-121391200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr11:121385200-121393000	Weak transcription	Brain Anterior Caudate	brain
39	chr11:121385400-121390800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:121385400-121392600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr11:121385400-121394600	Weak transcription	Brain Angular Gyrus	brain
42	chr11:121385400-121394600	Weak transcription	Fetal Lung	lung
43	chr11:121385600-121391000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr11:121385600-121392400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:121385600-121394000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr11:121385600-121396000	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr11:121385600-121396800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr11:121385600-121418200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr11:121385800-121390200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr11:121385800-121394400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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