Variant report

Variant	rs7302922
Chromosome Location	chr12:25349317-25349318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr12:25347216-25349605	SK-N-SH	brain:	n/a	chr12:25348081-25348096
2	POLR2A	chr12:25347727-25349494	PBDE	blood:	n/a	n/a
3	POLR2A	chr12:25347920-25349332	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:25347604-25351824	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr12:25347050-25349790	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr12:25348714-25349543	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr12:25347876-25349407	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:25346725..25349884-chr12:25402144..25405058,5	K562	blood:
2	chr12:25347765..25350303-chr12:25380801..25383112,2	K562	blood:

Variant related genes	Relation type
CASC1	TF binding region
ENSG00000133703	Chromatin interaction
ENSG00000268076	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10505960	0.84[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap]
rs10505980	0.83[GIH][hapmap];0.92[JPT][hapmap]
rs10842466	0.89[CHB][hapmap];0.80[CHD][hapmap]
rs10842492	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10842494	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs10842496	0.90[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap]
rs10842498	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10842499	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10842501	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842502	0.88[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10842504	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842512	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[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];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047888	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11047895	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11047896	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11047897	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11047899	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11047901	0.93[ASW][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11047902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11047905	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11047909	0.83[ASN][1000 genomes]
rs11047915	0.92[JPT][hapmap]
rs11047919	0.92[JPT][hapmap]
rs1137188	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1137189	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1137196	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11608657	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11611468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11832421	0.89[CHB][hapmap];0.80[CHD][hapmap];0.82[MEX][hapmap]
rs12226937	0.92[JPT][hapmap]
rs12245	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12368504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12423443	0.84[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap]
rs12424283	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12578773	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12579073	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12579681	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12579942	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12580030	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12581706	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12587	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12810577	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12813551	0.92[JPT][hapmap]
rs12814233	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs12815546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12820019	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12822857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13096	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]
rs17329025	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1908946	0.89[CHB][hapmap]
rs2291365	0.84[CHB][hapmap];0.80[CHD][hapmap];0.92[JPT][hapmap]
rs2352782	0.84[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap]
rs4246228	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4246229	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[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];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4494384	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4551857	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4559767	0.84[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap]
rs4963859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4963860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4963861	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5009909	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61762422	0.90[AFR][1000 genomes]
rs6487461	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6487464	0.83[GIH][hapmap];0.92[JPT][hapmap]
rs712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7137630	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7297103	0.84[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap]
rs7298636	0.90[JPT][hapmap]
rs7299998	0.84[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap]
rs7303094	0.83[ASN][1000 genomes]
rs7306769	0.84[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap]
rs7308865	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs7312739	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7955844	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8720	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9266	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9634100	0.84[CHB][hapmap];0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7302922	KRAS	cis	parietal	SCAN
rs7302922	LYRM5	cis	Thyroid	GTEx
rs7302922	LYRM5	cis	parietal	SCAN
rs7302922	LYRM5	cis	Whole Blood	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25347200-25349400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr12:25347400-25349400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:25347600-25349400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:25347600-25349400	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr12:25347600-25349400	Active TSS	Right Atrium	heart
6	chr12:25348000-25349400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:25348000-25349400	Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr12:25348600-25349400	Flanking Active TSS	Fetal Brain Female	brain
9	chr12:25348600-25349600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr12:25348600-25360000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:25348600-25402200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:25348600-25403200	Weak transcription	Spleen	Spleen
13	chr12:25348800-25349400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr12:25348800-25349400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:25348800-25349400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:25348800-25349400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:25348800-25349400	Flanking Active TSS	Fetal Lung	lung
18	chr12:25348800-25349400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr12:25348800-25349400	Flanking Active TSS	HUVEC	blood vessel
20	chr12:25348800-25349600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:25348800-25349600	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr12:25348800-25349600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:25348800-25349600	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr12:25348800-25349600	Flanking Active TSS	Dnd41	blood
25	chr12:25348800-25349800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:25348800-25349800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:25348800-25355400	Weak transcription	Small Intestine	intestine
28	chr12:25348800-25359400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:25348800-25360200	Weak transcription	Esophagus	oesophagus
30	chr12:25349000-25349400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr12:25349000-25349400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr12:25349000-25349400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:25349000-25349400	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr12:25349000-25349400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:25349000-25349400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr12:25349000-25349400	Flanking Active TSS	Liver	Liver
37	chr12:25349000-25349400	Enhancers	Fetal Brain Male	brain
38	chr12:25349000-25349400	Flanking Active TSS	Fetal Kidney	kidney
39	chr12:25349000-25349400	Flanking Active TSS	A549	lung
40	chr12:25349000-25349400	Flanking Active TSS	HepG2	liver
41	chr12:25349000-25349400	Flanking Active TSS	Osteobl	bone
42	chr12:25349000-25349600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:25349000-25349600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr12:25349000-25349600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:25349000-25349600	Weak transcription	Ovary	ovary
46	chr12:25349000-25349600	Flanking Active TSS	GM12878-XiMat	blood
47	chr12:25349000-25349600	Flanking Active TSS	Hela-S3	cervix
48	chr12:25349000-25349800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:25349000-25349800	Enhancers	Primary B cells from peripheral blood	blood
50	chr12:25349000-25349800	Enhancers	Primary T cells fromperipheralblood	blood

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