Variant report

Variant	rs10842466
Chromosome Location	chr12:25251381-25251382
allele	A/G
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	POLR2A	chr12:25250709-25251594	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:25251212-25251557	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:25250809-25252650	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000258546	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10505960	0.94[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap]
rs10771166	0.85[YRI][hapmap]
rs10842492	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs10842494	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs10842496	0.90[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap]
rs10842498	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs10842501	0.89[CHB][hapmap];0.80[CHD][hapmap]
rs10842502	0.83[CHB][hapmap]
rs10842504	0.83[CHB][hapmap]
rs10842505	0.88[CHB][hapmap]
rs11047823	0.94[ASN][1000 genomes]
rs11047824	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047846	0.81[ASN][1000 genomes]
rs11047865	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs11047887	0.89[CHB][hapmap];0.80[CHD][hapmap];0.84[TSI][hapmap]
rs11047888	0.89[CHB][hapmap]
rs11047894	0.89[CHB][hapmap]
rs11047901	0.89[CHB][hapmap]
rs11047902	0.89[CHB][hapmap]
rs1137188	0.89[CHB][hapmap]
rs11609915	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11609940	0.80[AFR][1000 genomes]
rs11611468	0.87[CHB][hapmap]
rs11832421	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11832456	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11834088	0.85[YRI][hapmap]
rs12368504	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs12423443	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs12425900	0.84[ASN][1000 genomes]
rs12579073	0.89[CHB][hapmap];0.86[CHD][hapmap];0.84[TSI][hapmap]
rs12579942	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs12587	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs12810577	0.89[CHB][hapmap]
rs12815546	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs12822857	0.89[CHB][hapmap]
rs12828225	0.84[ASN][1000 genomes]
rs13096	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs17329025	0.89[CHB][hapmap];0.80[CHD][hapmap]
rs1908946	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291365	0.95[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap]
rs2352782	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs4246229	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs4559767	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs4963859	0.89[CHB][hapmap]
rs4963860	0.89[CHB][hapmap]
rs712	0.89[CHB][hapmap]
rs7297103	0.95[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs7298636	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs7299998	0.95[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap]
rs7302922	0.89[CHB][hapmap];0.80[CHD][hapmap]
rs7306769	0.95[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap]
rs7308865	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs9266	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs9634100	0.94[CHB][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1041218	chr12:24972019-25304356	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv2757492	chr12:25233781-25252178	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv2759884	chr12:25233781-25252178	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10842466	LYRM5	cis	parietal	SCAN
rs10842466	PYROXD1	cis	parietal	SCAN
rs10842466	LYRM5	cis	Whole Blood	GTEx
rs10842466	KRAS	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25209400-25264400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:25210000-25262800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:25214400-25251800	Weak transcription	Fetal Intestine Large	intestine
4	chr12:25215000-25265000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:25229000-25253000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr12:25230000-25264600	Strong transcription	Fetal Thymus	thymus
7	chr12:25232200-25263600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr12:25238600-25263000	Weak transcription	Left Ventricle	heart
9	chr12:25238600-25265200	Weak transcription	Lung	lung
10	chr12:25239800-25253200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr12:25242800-25262200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:25243000-25259200	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr12:25246400-25252600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr12:25246400-25264000	Weak transcription	Ovary	ovary
15	chr12:25247400-25253000	Strong transcription	Primary B cells from peripheral blood	blood
16	chr12:25247400-25258400	Strong transcription	Primary T cells from cord blood	blood
17	chr12:25247800-25258000	Strong transcription	Primary B cells from cord blood	blood
18	chr12:25248000-25253000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:25248400-25262800	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr12:25248600-25252600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr12:25248600-25257800	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr12:25248600-25258600	Strong transcription	Primary hematopoietic stem cells	blood
23	chr12:25248600-25264400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:25248800-25251400	Strong transcription	GM12878-XiMat	blood
25	chr12:25248800-25255800	Strong transcription	Thymus	Thymus
26	chr12:25248800-25258000	Strong transcription	Dnd41	blood
27	chr12:25248800-25258400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:25248800-25259200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr12:25249000-25252200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr12:25249200-25261800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr12:25250000-25251400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr12:25250000-25253200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr12:25250600-25256000	Weak transcription	Esophagus	oesophagus
34	chr12:25250800-25251400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr12:25250800-25252000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:25250800-25252000	Strong transcription	Liver	Liver
37	chr12:25250800-25252000	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr12:25251000-25251400	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr12:25251000-25251400	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr12:25251000-25251800	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr12:25251000-25251800	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr12:25251000-25251800	Strong transcription	Pancreas	Pancrea
43	chr12:25251000-25252200	Strong transcription	Spleen	Spleen
44	chr12:25251000-25252400	Strong transcription	Adipose Nuclei	Adipose
45	chr12:25251000-25254000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr12:25251000-25254200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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