Variant report

Variant	rs12310541
Chromosome Location	chr12:31660568-31660569
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs11051457	0.91[AMR][1000 genomes]
rs1150944	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1150946	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1150947	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1150951	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1150952	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1150956	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1150957	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1150959	0.89[EUR][1000 genomes]
rs1150960	0.89[EUR][1000 genomes]
rs1150961	0.89[EUR][1000 genomes]
rs12299050	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12302576	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12305954	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1259215	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1259237	0.91[AMR][1000 genomes]
rs1259240	0.91[AMR][1000 genomes]
rs1259357	0.89[EUR][1000 genomes]
rs1259358	0.89[EUR][1000 genomes]
rs1259387	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1259388	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1259390	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1259391	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1259392	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1259394	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1259397	0.82[AMR][1000 genomes]
rs1259402	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1259403	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1259406	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1259407	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1259408	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1259410	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1259411	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1259412	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1259416	0.89[EUR][1000 genomes]
rs1259421	0.89[EUR][1000 genomes]
rs1259429	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1259436	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1259440	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1262389	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1262391	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1262392	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1267631	0.91[AMR][1000 genomes]
rs1267686	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1267688	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1267689	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1270211	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1271127	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1271657	0.91[AMR][1000 genomes]
rs1271661	0.89[EUR][1000 genomes]
rs1271662	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1273260	0.89[EUR][1000 genomes]
rs1677155	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1677156	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1677182	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1677188	0.89[EUR][1000 genomes]
rs1677190	0.89[EUR][1000 genomes]
rs1716193	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2568880	0.91[AMR][1000 genomes]
rs2568886	0.91[AMR][1000 genomes]
rs2617179	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2617189	0.91[AMR][1000 genomes]
rs2617192	0.91[AMR][1000 genomes]
rs2617194	0.91[AMR][1000 genomes]
rs2617210	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2679488	0.91[AMR][1000 genomes]
rs2679493	0.89[EUR][1000 genomes]
rs2679501	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2679502	0.91[AMR][1000 genomes]
rs2679503	0.91[AMR][1000 genomes]
rs2682461	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2682675	0.82[AMR][1000 genomes]
rs2682678	0.91[AMR][1000 genomes]
rs2682681	0.91[AMR][1000 genomes]
rs2682682	0.91[AMR][1000 genomes]
rs2682683	0.91[AMR][1000 genomes]
rs2682684	0.91[AMR][1000 genomes]
rs2682690	0.91[AMR][1000 genomes]
rs61663978	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs793172	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs793178	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs811088	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs971294	0.82[AMR][1000 genomes]
rs973510	0.91[AMR][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	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31583400-31662000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:31636200-31663000	Weak transcription	Aorta	Aorta
3	chr12:31642600-31670000	Weak transcription	Fetal Lung	lung
4	chr12:31647600-31661200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:31647800-31661400	Weak transcription	Brain Angular Gyrus	brain
6	chr12:31650800-31660800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:31651600-31661400	Weak transcription	HepG2	liver
8	chr12:31651600-31661800	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:31656400-31663200	Weak transcription	Left Ventricle	heart
10	chr12:31658800-31661600	Enhancers	Adipose Nuclei	Adipose
11	chr12:31658800-31671600	Weak transcription	Primary B cells from cord blood	blood
12	chr12:31659200-31663400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:31659200-31670600	Weak transcription	Fetal Intestine Small	intestine
14	chr12:31659400-31661400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr12:31659400-31662200	Enhancers	HUVEC	blood vessel
16	chr12:31659400-31662200	Enhancers	NH-A	brain
17	chr12:31659400-31662400	Enhancers	H9 Cell Line	embryonic stem cell
18	chr12:31659400-31662400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr12:31659400-31662600	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr12:31659400-31663000	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr12:31659400-31663000	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr12:31659400-31663200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:31659400-31663600	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr12:31659600-31660600	Enhancers	Fetal Heart	heart
25	chr12:31659600-31661600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:31659600-31662000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:31659600-31662000	Enhancers	NHEK	skin
28	chr12:31659600-31662400	Enhancers	Hela-S3	cervix
29	chr12:31659800-31661400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr12:31659800-31662200	Weak transcription	Right Ventricle	heart
31	chr12:31659800-31662800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:31659800-31663000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:31659800-31663600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:31660000-31660600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr12:31660000-31660800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:31660000-31660800	Weak transcription	Brain Substantia Nigra	brain
37	chr12:31660000-31661000	Enhancers	A549	lung
38	chr12:31660000-31662400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:31660000-31663800	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr12:31660000-31663800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:31660000-31663800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:31660000-31674600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr12:31660200-31661000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr12:31660200-31661000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:31660200-31661000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr12:31660200-31661000	Weak transcription	HMEC	breast
47	chr12:31660200-31661200	Weak transcription	Fetal Kidney	kidney
48	chr12:31660200-31661400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:31660200-31662200	Weak transcription	Right Atrium	heart
50	chr12:31660400-31661400	Weak transcription	H1 Cell Line	embryonic stem cell

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