Variant report

Variant	rs418941
Chromosome Location	chr12:118675292-118675293
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:118674302..118676883-chr12:118810896..118813058,3	MCF-7	breast:
2	chr12:118629722..118631578-chr12:118673558..118677291,3	K562	blood:
3	chr12:118674498..118676641-chr12:118709744..118711259,2	MCF-7	breast:
4	chr12:118673323..118676031-chr12:118677378..118679199,2	MCF-7	breast:
5	chr12:118673643..118676401-chr12:118686637..118689650,3	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1092854	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1151901	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1277175	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1726386	0.80[ASN][1000 genomes]
rs1726407	0.96[CEU][hapmap];0.84[TSI][hapmap]
rs2018619	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2088702	0.82[GIH][hapmap]
rs2249624	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs353885	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs353886	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs353887	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs353889	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs353890	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs353892	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs353896	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs364823	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs404566	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs410747	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs456228	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs461499	0.86[JPT][hapmap]
rs465735	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs484838	0.82[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs492939	0.82[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs494005	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs503548	0.82[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs523011	0.82[CEU][hapmap];0.80[CHB][hapmap]
rs566437	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs571113	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs575121	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs708862	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs708863	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7136004	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs7307953	0.90[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap]
rs7795	0.90[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap]
rs795473	0.88[ASN][1000 genomes]
rs795481	1.00[CEU][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs795482	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[ASN][1000 genomes]
rs7980628	0.84[JPT][hapmap]

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	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1035497	chr12:118599539-118732144	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv541612	chr12:118599539-118732144	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv524938	chr12:118624736-118740675	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1038224	chr12:118648415-118791388	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1040061	chr12:118648415-118800437	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	esv1815572	chr12:118664823-118685792	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs418941	GCN1L1	cis	cerebellum	SCAN
rs418941	FLJ20674	cis	multi-tissue	Pritchard

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118621000-118682600	Weak transcription	A549	lung
2	chr12:118628400-118697200	Weak transcription	Psoas Muscle	Psoas
3	chr12:118636800-118695000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:118637200-118700600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr12:118637200-118700800	Weak transcription	Fetal Muscle Leg	muscle
6	chr12:118637400-118684200	Weak transcription	Pancreas	Pancrea
7	chr12:118637400-118694200	Weak transcription	Brain Angular Gyrus	brain
8	chr12:118637400-118701400	Weak transcription	Spleen	Spleen
9	chr12:118637400-118703800	Weak transcription	Esophagus	oesophagus
10	chr12:118637400-118724000	Weak transcription	Aorta	Aorta
11	chr12:118638800-118687800	Weak transcription	Gastric	stomach
12	chr12:118650400-118690400	Weak transcription	Stomach Mucosa	stomach
13	chr12:118650600-118679400	Weak transcription	HUVEC	blood vessel
14	chr12:118652200-118727800	Weak transcription	NHLF	lung
15	chr12:118658000-118685400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:118659000-118693800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr12:118666200-118677000	Strong transcription	Dnd41	blood
18	chr12:118666800-118701000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:118667200-118704600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:118667400-118676600	Weak transcription	Hela-S3	cervix
21	chr12:118667800-118677600	Weak transcription	Fetal Intestine Small	intestine
22	chr12:118669000-118709000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr12:118669000-118725200	Weak transcription	K562	blood
24	chr12:118671200-118676000	Strong transcription	NHDF-Ad	bronchial
25	chr12:118671200-118677000	Strong transcription	Duodenum Mucosa	Duodenum
26	chr12:118671200-118677000	Strong transcription	Fetal Intestine Large	intestine
27	chr12:118671200-118677200	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr12:118671200-118701800	Weak transcription	Right Ventricle	heart
29	chr12:118671400-118675400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:118671400-118676800	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr12:118671400-118677000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr12:118671400-118677000	Strong transcription	Liver	Liver
33	chr12:118671400-118683400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr12:118672000-118676000	Strong transcription	Adipose Nuclei	Adipose
35	chr12:118672200-118676000	Strong transcription	Fetal Thymus	thymus
36	chr12:118672200-118676200	Strong transcription	HSMM	muscle
37	chr12:118672200-118677000	Strong transcription	Primary T cells from cord blood	blood
38	chr12:118672400-118676200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr12:118672400-118677600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr12:118672600-118675400	Weak transcription	Fetal Brain Male	brain
41	chr12:118672600-118676000	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr12:118672800-118681600	Weak transcription	Fetal Stomach	stomach
43	chr12:118673200-118698800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr12:118673200-118701600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr12:118673400-118675600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr12:118673400-118675800	Weak transcription	NH-A	brain
47	chr12:118673400-118677000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:118673400-118681800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr12:118673400-118688200	Weak transcription	Brain Substantia Nigra	brain
50	chr12:118673400-118692000	Weak transcription	Brain Anterior Caudate	brain

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