Variant report

Variant	rs2724635
Chromosome Location	chr12:11899973-11899974
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:11898044..11900698-chr12:11957221..11959288,2	MCF-7	breast:
2	chr12:11880587..11883576-chr12:11898372..11900134,2	MCF-7	breast:
3	chr12:11880124..11883020-chr12:11899873..11902243,3	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1009951	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1009953	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1009954	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.99[ASN][1000 genomes]
rs10743967	0.90[ASN][1000 genomes]
rs10845410	0.87[EUR][1000 genomes]
rs11054433	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs11615175	0.84[EUR][1000 genomes]
rs12369491	0.88[CEU][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs17818461	0.88[CEU][hapmap];0.91[CHB][hapmap]
rs2051525	1.00[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs2187641	0.85[CEU][hapmap]
rs2187642	0.87[CHB][hapmap];0.93[CHD][hapmap]
rs2416883	0.81[CEU][hapmap]
rs2724600	0.84[EUR][1000 genomes]
rs2724645	0.89[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2856322	0.95[CHB][hapmap]
rs2856324	0.89[CEU][hapmap];0.95[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2856338	0.84[CEU][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs2856344	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2860431	0.85[CEU][hapmap]
rs4763719	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[MEX][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs762717	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[MEX][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870039	chr12:11800363-11996598	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
2	nsv1053609	chr12:11898099-11933906	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2724635	C12orf36	cis	parietal	SCAN
rs2724635	OLR1	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11873200-11902400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:11873200-11909400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:11882400-11902600	Weak transcription	Fetal Muscle Leg	muscle
4	chr12:11882400-11903200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr12:11883800-11906000	Weak transcription	Liver	Liver
6	chr12:11885200-11906200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:11885600-11905200	Weak transcription	Fetal Intestine Large	intestine
8	chr12:11885800-11911600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr12:11886000-11900000	Weak transcription	Colonic Mucosa	Colon
10	chr12:11889800-11901800	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr12:11890000-11902400	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:11893200-11915000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr12:11893800-11901200	Enhancers	HMEC	breast
14	chr12:11894600-11905200	Weak transcription	Fetal Intestine Small	intestine
15	chr12:11894600-11905400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:11894600-11905400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr12:11894600-11906200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:11894600-11908400	Weak transcription	Psoas Muscle	Psoas
19	chr12:11894800-11906000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:11894800-11906600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:11895000-11906000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr12:11895000-11906800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:11895000-11912600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr12:11895400-11906000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:11895400-11914400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:11895600-11908800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr12:11895800-11901200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:11896000-11906200	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr12:11896200-11900200	Enhancers	Rectal Smooth Muscle	rectum
30	chr12:11896400-11900400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:11896400-11902800	Enhancers	Primary B cells from peripheral blood	blood
32	chr12:11896600-11900400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:11896800-11900600	Enhancers	NHEK	skin
34	chr12:11896800-11901800	Enhancers	Spleen	Spleen
35	chr12:11897000-11901600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:11897000-11905400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:11897000-11906400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:11897000-11906400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:11897000-11908800	Weak transcription	Brain Anterior Caudate	brain
40	chr12:11897200-11901000	Weak transcription	Fetal Lung	lung
41	chr12:11897200-11901400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr12:11897200-11902600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:11897200-11905400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:11897400-11901800	Enhancers	HUVEC	blood vessel
45	chr12:11897400-11902600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:11897600-11902600	Weak transcription	Right Ventricle	heart
47	chr12:11897600-11904200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr12:11897600-11904600	Enhancers	Thymus	Thymus
49	chr12:11897800-11900000	Weak transcription	Lung	lung
50	chr12:11897800-11904200	Weak transcription	H9 Cell Line	embryonic stem cell

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