Variant report

Variant	rs12132114
Chromosome Location	chr1:92293721-92293722
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1017956	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1017957	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs10493858	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783036	0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs10783037	0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs10783040	0.86[ASN][1000 genomes]
rs10874976	0.91[CEU][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.87[EUR][1000 genomes]
rs10874981	0.89[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs10874983	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10874996	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10874999	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10875001	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11165560	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165587	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11165594	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12089918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12133180	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1411276	0.95[CEU][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs2004067	0.87[EUR][1000 genomes]
rs2129975	0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2297142	0.90[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes]
rs2489190	0.82[ASN][1000 genomes]
rs2634031	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2799537	0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4658275	0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4658276	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686126	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6687561	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6691098	0.91[CEU][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1005917	chr1:92189945-92378683	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv949449	chr1:92211020-92585831	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv524845	chr1:92215725-92598705	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv462517	chr1:92215725-92598705	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv546810	chr1:92215725-92598705	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1006318	chr1:92216408-92608324	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv432498	chr1:92218245-92618323	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1004570	chr1:92220544-92622129	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv1007661	chr1:92220544-92655952	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	nsv1014837	chr1:92233905-92618839	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv535031	chr1:92233905-92618839	Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	nsv1012134	chr1:92235485-92598800	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
18	nsv546818	chr1:92236048-92579206	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
19	nsv546819	chr1:92256626-92558583	Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	nsv546820	chr1:92273644-92558583	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
21	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
22	nsv1007270	chr1:92289298-92598800	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12132114	BARHL2	cis	cerebellum	SCAN
rs12132114	LRRC8B	cis	parietal	SCAN
rs12132114	FAM69A	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92279600-92294000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr1:92284200-92295400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:92285800-92295600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:92286000-92295600	Weak transcription	Fetal Stomach	stomach
5	chr1:92287600-92294000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:92287600-92296000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr1:92291600-92293800	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr1:92291600-92294200	Enhancers	Pancreas	Pancrea
9	chr1:92291600-92295000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:92291600-92296600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:92291800-92293800	Enhancers	NHLF	lung
12	chr1:92291800-92294600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:92291800-92294600	Enhancers	Fetal Intestine Small	intestine
14	chr1:92292000-92294000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:92292000-92294000	Weak transcription	Right Ventricle	heart
16	chr1:92292000-92294400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr1:92292200-92294200	Weak transcription	Ovary	ovary
18	chr1:92292200-92295000	Enhancers	Fetal Intestine Large	intestine
19	chr1:92292400-92297000	Enhancers	Placenta	Placenta
20	chr1:92292600-92293800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:92292600-92293800	Enhancers	Liver	Liver
22	chr1:92292600-92294000	Enhancers	NHEK	skin
23	chr1:92292600-92294200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:92292600-92294200	Enhancers	Brain Anterior Caudate	brain
25	chr1:92292600-92294800	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr1:92292800-92293800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:92292800-92293800	Enhancers	Brain Angular Gyrus	brain
28	chr1:92292800-92294200	Weak transcription	Lung	lung
29	chr1:92292800-92294400	Enhancers	Stomach Mucosa	stomach
30	chr1:92292800-92294600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:92292800-92295000	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr1:92293000-92294000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:92293000-92294000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr1:92293000-92294200	Enhancers	Fetal Lung	lung
35	chr1:92293000-92294600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:92293000-92294600	Enhancers	K562	blood
37	chr1:92293000-92295600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr1:92293000-92295800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:92293000-92295800	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr1:92293000-92296000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:92293000-92296200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:92293200-92293800	Enhancers	Brain Substantia Nigra	brain
43	chr1:92293200-92294800	Enhancers	Adipose Nuclei	Adipose
44	chr1:92293200-92296200	Enhancers	Small Intestine	intestine
45	chr1:92293200-92296800	Enhancers	Right Atrium	heart
46	chr1:92293200-92297000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:92293400-92294000	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr1:92293400-92294400	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr1:92293400-92295000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr1:92293400-92295000	Flanking Active TSS	HepG2	liver

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