Variant report

Variant	rs11897611
Chromosome Location	chr2:20775317-20775318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20768678..20771590-chr2:20774793..20776320,2	K562	blood:
2	chr2:20756784..20758920-chr2:20774602..20776953,2	K562	blood:
3	chr2:20771832..20774645-chr2:20774771..20777739,3	K562	blood:
4	chr2:20772999..20776929-chr2:20778925..20783592,5	MCF-7	breast:
5	chr2:20672376..20674639-chr2:20775107..20777593,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10166792	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10177787	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10177834	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs10190705	0.86[ASN][1000 genomes]
rs10195324	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10195722	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200207	0.85[ASN][1000 genomes]
rs11096676	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11096677	0.90[ASN][1000 genomes]
rs11096679	0.86[CHB][hapmap]
rs1123781	0.88[ASN][1000 genomes]
rs11691255	0.86[ASN][1000 genomes]
rs11885969	0.86[CHB][hapmap]
rs12472478	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621527	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13013281	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs13031724	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs13032956	0.82[JPT][hapmap]
rs13422371	0.86[ASN][1000 genomes]
rs16987857	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16987878	0.92[JPT][hapmap]
rs16987880	0.93[JPT][hapmap]
rs16987884	0.93[JPT][hapmap]
rs1809132	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2882035	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2882036	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4666315	0.90[ASN][1000 genomes]
rs4666426	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4666427	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4666428	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4666429	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4666430	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666431	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666436	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs56129345	0.84[ASN][1000 genomes]
rs6715159	0.86[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs6722960	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs72782365	0.83[ASN][1000 genomes]
rs766474	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs921599	0.86[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1012037	chr2:20770850-20824893	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535598	chr2:20770850-20824893	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11897611		cis	Lymphoblastoid	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20764400-20778200	Enhancers	HepG2	liver
2	chr2:20765600-20780800	Enhancers	Adipose Nuclei	Adipose
3	chr2:20765800-20786200	Enhancers	HUVEC	blood vessel
4	chr2:20766400-20776000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr2:20766800-20780800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr2:20766800-20781000	Enhancers	Left Ventricle	heart
7	chr2:20767000-20781000	Enhancers	Right Atrium	heart
8	chr2:20767200-20776600	Enhancers	Right Ventricle	heart
9	chr2:20767400-20778200	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr2:20767800-20778600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:20767800-20782600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:20768600-20777200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:20769200-20777000	Weak transcription	HMEC	breast
14	chr2:20769400-20780000	Enhancers	Fetal Intestine Large	intestine
15	chr2:20769800-20781000	Enhancers	Fetal Muscle Leg	muscle
16	chr2:20771600-20777200	Weak transcription	Psoas Muscle	Psoas
17	chr2:20771600-20777400	Weak transcription	Small Intestine	intestine
18	chr2:20772600-20781000	Enhancers	Placenta	Placenta
19	chr2:20772600-20785800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:20772800-20775400	Enhancers	Brain Cingulate Gyrus	brain
21	chr2:20772800-20775400	Enhancers	Brain Hippocampus Middle	brain
22	chr2:20772800-20775400	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr2:20772800-20779400	Weak transcription	Liver	Liver
24	chr2:20772800-20780800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:20773000-20777800	Weak transcription	Pancreas	Pancrea
26	chr2:20773000-20781000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:20773200-20775600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:20773400-20775400	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr2:20773400-20775400	Enhancers	Brain Germinal Matrix	brain
30	chr2:20773400-20775400	Enhancers	Colon Smooth Muscle	Colon
31	chr2:20773400-20775600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:20773400-20781200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr2:20773600-20776000	Enhancers	Duodenum Mucosa	Duodenum
34	chr2:20773600-20780000	Enhancers	Spleen	Spleen
35	chr2:20773600-20780200	Enhancers	Fetal Heart	heart
36	chr2:20773600-20781000	Enhancers	Lung	lung
37	chr2:20774000-20775600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:20774000-20775600	Enhancers	Stomach Smooth Muscle	stomach
39	chr2:20774000-20777000	Weak transcription	NHEK	skin
40	chr2:20774000-20777800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:20774000-20777800	Weak transcription	HSMM	muscle
42	chr2:20774000-20778400	Weak transcription	Fetal Kidney	kidney
43	chr2:20774200-20777400	Weak transcription	Osteobl	bone
44	chr2:20774400-20775400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:20774400-20776200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr2:20774400-20777200	Weak transcription	Esophagus	oesophagus
47	chr2:20774400-20777400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr2:20774400-20777600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:20774400-20777600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:20774400-20778400	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links