Variant report

Variant	rs10842459
Chromosome Location	chr12:25227415-25227416
allele	C/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	chr12:25226986-25227672	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:25225156-25229392	GM12878	blood:	n/a	n/a
3	FOS	chr12:25227087-25227425	MCF10A-Er-Src	breast:	n/a	chr12:25227247-25227257 chr12:25227247-25227257
4	BCLAF1	chr12:25227400-25228325	GM12878	blood:	n/a	n/a
5	STAT3	chr12:25227084-25227432	MCF10A-Er-Src	breast:	n/a	chr12:25227131-25227138
6	POLR2A	chr12:25227399-25227424	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:25227139-25227452	GM12878	blood:	n/a	n/a
8	TBL1XR1	chr12:25227284-25228341	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:25224381-25228181	GM12891	blood:	n/a	n/a
10	WRNIP1	chr12:25227190-25227455	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
LRMP	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10743533	1.00[ASW][hapmap];0.84[CEU][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10743534	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10743535	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10743536	0.95[JPT][hapmap];0.94[MKK][hapmap]
rs10771163	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10842455	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10842456	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10842457	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10842458	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842460	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[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];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11047799	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11047800	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11047811	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047813	0.95[JPT][hapmap]
rs12315725	0.89[EUR][1000 genomes]
rs12813199	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1497249	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2054767	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2291801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7955576	0.95[JPT][hapmap]
rs7969226	0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1051319	chr12:24921100-25238936	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1037288	chr12:24941350-25238936	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv541428	chr12:24941350-25238936	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10842459	CMAS	cis	parietal	SCAN
rs10842459	LRMP	cis	lymphoblastoid	seeQTL
rs10842459	LRMP	cis	brain	seeQTL
rs10842459	LYRM5	cis	parietal	SCAN

Chromatin state (count:42 , 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	chr12:25212000-25250800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr12:25214400-25245600	Weak transcription	Ovary	ovary
5	chr12:25214400-25251800	Weak transcription	Fetal Intestine Large	intestine
6	chr12:25215000-25265000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:25215400-25228000	Strong transcription	Fetal Thymus	thymus
8	chr12:25218600-25239200	Weak transcription	Fetal Intestine Small	intestine
9	chr12:25221600-25229200	Genic enhancers	Primary B cells from peripheral blood	blood
10	chr12:25221600-25235800	Weak transcription	Liver	Liver
11	chr12:25222400-25228000	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr12:25222400-25236000	Weak transcription	Adipose Nuclei	Adipose
13	chr12:25222800-25232200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr12:25223000-25238000	Weak transcription	Spleen	Spleen
15	chr12:25223400-25232200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:25223400-25235400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr12:25223600-25232000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr12:25223600-25232200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr12:25223600-25232200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr12:25224000-25227800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr12:25224000-25228800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:25224000-25232200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr12:25224200-25228400	Enhancers	Stomach Mucosa	stomach
24	chr12:25224600-25230600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr12:25224600-25241600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:25225200-25227600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
27	chr12:25225400-25228200	Genic enhancers	Primary B cells from cord blood	blood
28	chr12:25225400-25228400	Weak transcription	Esophagus	oesophagus
29	chr12:25225400-25232200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:25225400-25237800	Weak transcription	Lung	lung
31	chr12:25225600-25229000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:25225800-25227600	Genic enhancers	Primary hematopoietic stem cells	blood
33	chr12:25226000-25232000	Weak transcription	Dnd41	blood
34	chr12:25226600-25230400	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr12:25226600-25232000	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr12:25226600-25232200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr12:25226800-25230800	Weak transcription	Primary T cells from cord blood	blood
38	chr12:25227000-25227600	Genic enhancers	Primary monocytes fromperipheralblood	blood
39	chr12:25227000-25227800	Genic enhancers	Monocytes-CD14+_RO01746	blood
40	chr12:25227200-25227800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:25227400-25228400	Weak transcription	Thymus	Thymus
42	chr12:25227400-25251000	Weak transcription	Pancreas	Pancrea

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