Variant report

Variant	rs2187499
Chromosome Location	chr11:76683305-76683306
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10899314	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11236997	0.84[AFR][1000 genomes]
rs11237030	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11602065	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs11605656	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11606034	0.84[AFR][1000 genomes]
rs11606467	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12223477	0.82[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1225138	0.80[GIH][hapmap]
rs17812687	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1945084	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1945085	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2048954	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2279518	0.82[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs2372387	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3740766	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3740768	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3862808	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4016126	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4944130	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4944133	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4945128	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55743360	0.88[AFR][1000 genomes]
rs55798841	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55977032	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56129156	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56789915	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61895513	0.80[AFR][1000 genomes]
rs61900090	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61900119	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61900120	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7118398	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519700	chr11:76637651-76709407	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1042924	chr11:76659477-76709407	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1040833	chr11:76667160-76709407	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv396	chr11:76670116-76702745	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1802222	chr11:76683305-76709407	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2187499	ALG8	cis	parietal	SCAN
rs2187499	ACER3	cis	lymphoblastoid	seeQTL
rs2187499	SNORD15B	cis	parietal	SCAN
rs2187499	GDPD5	cis	parietal	SCAN
rs2187499	CAPN5	cis	parietal	SCAN
rs2187499	C2CD3	cis	parietal	SCAN
rs2187499	KLHL35	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76631400-76688400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:76645800-76683800	Weak transcription	Esophagus	oesophagus
3	chr11:76646600-76688000	Weak transcription	HMEC	breast
4	chr11:76657200-76688400	Weak transcription	Gastric	stomach
5	chr11:76660000-76710800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr11:76665800-76688400	Weak transcription	Right Ventricle	heart
7	chr11:76666800-76695400	Weak transcription	NHEK	skin
8	chr11:76672200-76697800	Weak transcription	Left Ventricle	heart
9	chr11:76672400-76696000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr11:76673000-76689600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr11:76673800-76690400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr11:76674000-76688600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr11:76674200-76683800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr11:76674400-76696000	Weak transcription	Small Intestine	intestine
15	chr11:76675000-76683800	Weak transcription	Placenta	Placenta
16	chr11:76675000-76688600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:76675000-76689800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr11:76675000-76691600	Weak transcription	Fetal Lung	lung
19	chr11:76675000-76721800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr11:76675000-76725600	Weak transcription	A549	lung
21	chr11:76675000-76729600	Weak transcription	Brain Angular Gyrus	brain
22	chr11:76675200-76684000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr11:76675200-76688000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr11:76675200-76688000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr11:76675200-76688200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr11:76675400-76688600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:76675400-76688800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr11:76675400-76689000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr11:76681600-76684200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr11:76681800-76683400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr11:76681800-76683400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
32	chr11:76682000-76683400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr11:76682800-76683400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr11:76683000-76683800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr11:76683000-76684200	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr11:76683000-76684200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr11:76683000-76688000	Weak transcription	Primary B cells from cord blood	blood
38	chr11:76683000-76736400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr11:76683200-76683400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr11:76683200-76688000	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr11:76683200-76688600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr11:76683200-76729200	Weak transcription	Brain Hippocampus Middle	brain

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