Variant report

Variant	rs12091012
Chromosome Location	chr1:174207948-174207949
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174148713..174151052-chr1:174207157..174208937,2	MCF-7	breast:
2	chr1:174207103..174211366-chr1:174211395..174216784,8	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10798307	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10912735	0.81[AMR][1000 genomes]
rs10912737	0.82[AMR][1000 genomes]
rs10912740	0.82[AMR][1000 genomes]
rs10912741	0.83[AMR][1000 genomes]
rs10912746	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10912747	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10912750	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10912751	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10912754	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11802158	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11807537	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12059434	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12074276	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12076453	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12076771	0.81[AMR][1000 genomes]
rs12079687	0.81[AMR][1000 genomes]
rs12079689	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12080977	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12081445	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12082461	0.82[AMR][1000 genomes]
rs12083540	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12085311	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12087808	0.82[AMR][1000 genomes]
rs12091155	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12091157	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12093691	0.81[AMR][1000 genomes]
rs12354141	0.81[AMR][1000 genomes]
rs1591944	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16846816	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1934681	0.82[AMR][1000 genomes]
rs2103640	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2860907	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3086	0.82[AMR][1000 genomes]
rs4233171	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4607949	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4650959	0.82[AMR][1000 genomes]
rs4650968	0.90[EUR][1000 genomes]
rs4650969	0.90[EUR][1000 genomes]
rs4650981	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4652275	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55698100	0.89[EUR][1000 genomes]
rs56338048	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59649440	0.84[EUR][1000 genomes]
rs6425277	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6666588	0.90[EUR][1000 genomes]
rs6678286	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6692437	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs724888	0.82[AMR][1000 genomes]
rs724889	0.82[AMR][1000 genomes]
rs72711487	0.83[AMR][1000 genomes]
rs72711501	0.89[EUR][1000 genomes]
rs72713503	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72713504	0.90[EUR][1000 genomes]
rs72713505	0.90[EUR][1000 genomes]
rs7535987	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7551605	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1008314	chr1:174080192-174311023	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv535207	chr1:174080192-174311023	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	esv1799250	chr1:174119038-174484277	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv1800060	chr1:174132703-174501836	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv465672	chr1:174133251-174469905	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv548194	chr1:174133251-174469905	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv470746	chr1:174150850-174469905	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1001803	chr1:174176164-174367747	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1008993	chr1:174180019-174331358	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	nsv528675	chr1:174195629-174219398	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv872553	chr1:174195629-174373379	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	esv3349547	chr1:174203279-174207977	Weak transcription Active TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12091012	RABGAP1L	cis	Esophagus Muscularis	GTEx
rs12091012	RP11-160H22.5	cis	Thyroid	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174176000-174222400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:174176800-174222400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:174177200-174212000	Weak transcription	Lung	lung
4	chr1:174178600-174212200	Weak transcription	Psoas Muscle	Psoas
5	chr1:174186600-174216600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:174186800-174208000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:174186800-174212800	Weak transcription	Fetal Heart	heart
8	chr1:174186800-174213200	Weak transcription	Ovary	ovary
9	chr1:174186800-174217000	Weak transcription	Brain Angular Gyrus	brain
10	chr1:174186800-174232000	Weak transcription	HSMMtube	muscle
11	chr1:174187000-174217000	Weak transcription	Pancreas	Pancrea
12	chr1:174187400-174208000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:174188600-174213400	Weak transcription	Spleen	Spleen
14	chr1:174189000-174232000	Weak transcription	HSMM	muscle
15	chr1:174189200-174216800	Weak transcription	Small Intestine	intestine
16	chr1:174189600-174215400	Weak transcription	NH-A	brain
17	chr1:174191000-174215600	Weak transcription	Fetal Brain Male	brain
18	chr1:174191400-174215400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:174191400-174232000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:174191600-174208600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:174191600-174213400	Weak transcription	Thymus	Thymus
22	chr1:174191600-174232200	Weak transcription	Brain Substantia Nigra	brain
23	chr1:174191800-174208000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:174191800-174215600	Weak transcription	Brain Anterior Caudate	brain
25	chr1:174192000-174208400	Weak transcription	Fetal Kidney	kidney
26	chr1:174192000-174208600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:174192000-174215200	Weak transcription	HMEC	breast
28	chr1:174192000-174219400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:174192200-174208200	Weak transcription	HepG2	liver
30	chr1:174192200-174213200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:174192400-174224600	Weak transcription	Fetal Thymus	thymus
32	chr1:174192600-174213600	Weak transcription	Fetal Intestine Small	intestine
33	chr1:174193200-174212800	Weak transcription	Hela-S3	cervix
34	chr1:174197000-174213400	Weak transcription	Colonic Mucosa	Colon
35	chr1:174198800-174213400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:174199400-174213400	Weak transcription	Gastric	stomach
37	chr1:174200600-174216000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr1:174200800-174213600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:174200800-174249200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:174201000-174208000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr1:174201000-174209400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr1:174201000-174213200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:174201000-174213400	Weak transcription	Aorta	Aorta
44	chr1:174201000-174217600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:174201000-174221800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr1:174201000-174249800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr1:174201200-174208000	Weak transcription	Placenta	Placenta
48	chr1:174201200-174212200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr1:174201200-174213400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:174201200-174218200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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