Variant report

Variant	rs11684636
Chromosome Location	chr2:233691895-233691896
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10176930	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10190211	0.84[ASN][1000 genomes]
rs10207739	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10933407	0.84[ASN][1000 genomes]
rs10933408	0.84[ASN][1000 genomes]
rs11679581	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11685169	0.84[ASN][1000 genomes]
rs11689661	0.89[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694434	0.88[ASN][1000 genomes]
rs11695762	0.92[ASN][1000 genomes]
rs11904619	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12052869	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12328140	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12694915	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12694916	0.84[ASN][1000 genomes]
rs12988087	0.96[ASN][1000 genomes]
rs13035517	1.00[CHB][hapmap]
rs13383733	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap]
rs13386650	0.80[ASN][1000 genomes]
rs13387762	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13390935	0.86[CHB][hapmap]
rs13401578	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13408229	0.92[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13412034	0.80[ASN][1000 genomes]
rs13412513	0.84[ASN][1000 genomes]
rs13424896	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs13425525	0.92[ASN][1000 genomes]
rs13425918	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13429857	0.80[ASN][1000 genomes]
rs1446307	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2289914	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs2289915	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs2292724	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap]
rs2292725	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs2293782	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2305139	0.88[ASN][1000 genomes]
rs28491817	0.88[ASN][1000 genomes]
rs34063802	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs34832091	0.84[ASN][1000 genomes]
rs35778045	0.88[ASN][1000 genomes]
rs35785837	0.84[ASN][1000 genomes]
rs35928329	0.84[ASN][1000 genomes]
rs41266951	0.88[ASN][1000 genomes]
rs56054779	0.88[ASN][1000 genomes]
rs62193305	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6747479	1.00[JPT][hapmap]
rs73005582	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7557131	0.80[ASN][1000 genomes]
rs9288675	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9288676	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs9808146	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9973586	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv460134	chr2:233639909-233714686	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv584696	chr2:233639909-233714686	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv584697	chr2:233684097-233733352	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11684636	HJURP	cis	cerebellum	SCAN
rs11684636	COPS7B	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233665000-233692600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:233665800-233734200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:233667600-233726400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:233667800-233693400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:233669000-233701800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:233669400-233703600	Strong transcription	Liver	Liver
7	chr2:233669800-233692000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:233670000-233701600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr2:233670200-233692200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:233670200-233699600	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr2:233670200-233702600	Strong transcription	HepG2	liver
12	chr2:233670600-233692600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:233670800-233700200	Strong transcription	Duodenum Mucosa	Duodenum
14	chr2:233671000-233692000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:233671000-233700400	Strong transcription	Fetal Intestine Large	intestine
16	chr2:233678200-233698200	Weak transcription	Stomach Mucosa	stomach
17	chr2:233679400-233693400	Strong transcription	HSMM	muscle
18	chr2:233679600-233692200	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr2:233680600-233698600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr2:233681600-233702400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr2:233681800-233694800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:233681800-233695400	Weak transcription	Esophagus	oesophagus
23	chr2:233681800-233695600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:233681800-233695600	Weak transcription	Right Ventricle	heart
25	chr2:233681800-233695800	Weak transcription	Gastric	stomach
26	chr2:233681800-233702200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr2:233682000-233695400	Weak transcription	Small Intestine	intestine
28	chr2:233683000-233695400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:233683000-233695400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:233683600-233695800	Weak transcription	HMEC	breast
31	chr2:233684400-233702400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:233684600-233694000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:233684800-233694400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:233686200-233694800	Weak transcription	Spleen	Spleen
35	chr2:233686200-233696600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr2:233686200-233696600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:233686200-233697600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:233686800-233692200	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr2:233686800-233694800	Weak transcription	NHDF-Ad	bronchial
40	chr2:233687000-233700400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr2:233687400-233692200	Strong transcription	Primary B cells from cord blood	blood
42	chr2:233687400-233692400	Strong transcription	Adipose Nuclei	Adipose
43	chr2:233687600-233702400	Strong transcription	Primary B cells from peripheral blood	blood
44	chr2:233687800-233692200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:233687800-233692400	Strong transcription	Primary hematopoietic stem cells	blood
46	chr2:233687800-233701600	Strong transcription	Fetal Thymus	thymus
47	chr2:233688000-233702400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:233688200-233692200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr2:233688200-233692200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:233688600-233695600	Weak transcription	NHLF	lung

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