Variant report

Variant	rs13096
Chromosome Location	chr12:25359841-25359842
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:25357761..25359956-chr12:25367991..25370766,2	K562	blood:
2	chr12:25359301..25361525-chr12:25535610..25537656,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10505960	0.84[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs10505980	0.83[GIH][hapmap];0.92[JPT][hapmap]
rs10842466	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs10842492	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10842494	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs10842496	0.93[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap]
rs10842498	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10842499	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10842501	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10842502	0.88[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10842504	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10842505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10842512	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10842514	0.92[JPT][hapmap]
rs11047824	0.89[CHB][hapmap]
rs11047865	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs11047887	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.89[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11047888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11047894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047895	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047896	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047897	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047899	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11047901	0.80[ASW][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11047905	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11047909	0.87[ASN][1000 genomes]
rs11047915	0.92[JPT][hapmap]
rs11047919	0.92[JPT][hapmap]
rs1137188	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1137189	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1137196	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11608657	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11832421	0.89[CHB][hapmap];0.83[CHD][hapmap];0.82[MEX][hapmap]
rs12226937	0.92[JPT][hapmap]
rs12245	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12423443	0.84[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap]
rs12424283	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12578773	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12579073	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12579681	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12579942	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12580030	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12581706	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12810577	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12813551	0.92[JPT][hapmap]
rs12815546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12820019	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12822857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17329025	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1908946	0.89[CHB][hapmap]
rs2291365	0.84[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap]
rs2352782	0.84[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap]
rs4246228	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4246229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4494384	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4551857	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4559767	0.84[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap]
rs4963859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4963860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4963861	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5009909	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6487461	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487464	0.83[GIH][hapmap];0.92[JPT][hapmap]
rs712	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137630	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7297103	0.84[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap]
rs7298636	0.90[JPT][hapmap]
rs7299998	0.84[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap]
rs7302922	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7306769	0.84[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap]
rs7308865	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs7312739	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7955844	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8720	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9634100	0.84[CHB][hapmap];0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898922	chr12:25274593-25408047	Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1048631	chr12:25353517-25378661	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv898923	chr12:25357680-25397282	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv898924	chr12:25357680-25398972	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv557798	chr12:25359841-25397282	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13096	KRAS	cis	parietal	SCAN
rs13096	LYRM5	cis	parietal	SCAN
rs13096	LYRM5	cis	Thyroid	GTEx
rs13096	LYRM5	cis	Whole Blood	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25348600-25360000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:25348600-25402200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:25348600-25403200	Weak transcription	Spleen	Spleen
4	chr12:25348800-25360200	Weak transcription	Esophagus	oesophagus
5	chr12:25349000-25360000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr12:25349000-25360000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:25349000-25360400	Weak transcription	Psoas Muscle	Psoas
8	chr12:25349000-25369200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:25349000-25372800	Weak transcription	Aorta	Aorta
10	chr12:25349000-25374200	Weak transcription	Lung	lung
11	chr12:25349000-25386000	Weak transcription	Left Ventricle	heart
12	chr12:25349000-25402400	Weak transcription	Right Ventricle	heart
13	chr12:25349200-25360800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr12:25349200-25362400	Weak transcription	Colonic Mucosa	Colon
15	chr12:25349200-25363200	Weak transcription	Brain Substantia Nigra	brain
16	chr12:25349200-25363400	Weak transcription	Stomach Mucosa	stomach
17	chr12:25349400-25367400	Weak transcription	Fetal Stomach	stomach
18	chr12:25349400-25388200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:25349400-25388600	Weak transcription	NHLF	lung
20	chr12:25349400-25393800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr12:25349400-25396000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr12:25349400-25401800	Weak transcription	Fetal Brain Male	brain
23	chr12:25349400-25402600	Weak transcription	Brain Germinal Matrix	brain
24	chr12:25349600-25360000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:25349600-25360000	Weak transcription	Fetal Brain Female	brain
26	chr12:25349600-25360800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr12:25349600-25364600	Weak transcription	Colon Smooth Muscle	Colon
28	chr12:25349600-25389000	Weak transcription	Brain Angular Gyrus	brain
29	chr12:25349600-25394600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:25349600-25402600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:25349600-25402600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr12:25349600-25402600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:25349600-25402600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr12:25349800-25360000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:25349800-25360000	Weak transcription	Thymus	Thymus
36	chr12:25349800-25360200	Weak transcription	Fetal Muscle Leg	muscle
37	chr12:25349800-25360400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr12:25349800-25360400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr12:25349800-25379200	Weak transcription	Brain Anterior Caudate	brain
40	chr12:25349800-25386200	Weak transcription	Hela-S3	cervix
41	chr12:25349800-25390200	Weak transcription	K562	blood
42	chr12:25350000-25372600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr12:25350000-25402800	Weak transcription	Ovary	ovary
44	chr12:25353200-25378800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr12:25354000-25402400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr12:25354400-25360000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:25354400-25360000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:25354400-25360000	Weak transcription	NH-A	brain
49	chr12:25354400-25368200	Weak transcription	HUVEC	blood vessel
50	chr12:25354400-25369000	Weak transcription	Brain Hippocampus Middle	brain

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