Variant report

Variant	rs12547922
Chromosome Location	chr8:99542022-99542023
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	FOS	chr8:99541876-99542076	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr8:99541841-99542040	MCF10A-Er-Src	breast:	n/a	n/a
3	TBP	chr8:99541833-99542068	K562	blood:	n/a	n/a
4	HEY1	chr8:99541950-99542200	K562	blood:	n/a	n/a
5	MAFK	chr8:99541974-99542206	HepG2	liver:	n/a	n/a
6	POLR2A	chr8:99541827-99542246	K562	blood:	n/a	n/a
7	FOS	chr8:99541860-99542060	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:99527652..99530534-chr8:99540063..99542504,2	MCF-7	breast:
2	chr8:99540019..99542563-chr8:99545669..99547224,2	K562	blood:

Variant related genes	Relation type
STK3	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10086870	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10098835	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10099978	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10100346	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10100378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10100546	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10100577	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10101919	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10108828	0.86[JPT][hapmap]
rs10111264	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10441501	0.81[CEU][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10955174	0.81[EUR][1000 genomes]
rs10955175	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10955176	0.82[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10955177	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10955178	0.80[AMR][1000 genomes]
rs10955179	0.82[JPT][hapmap];0.80[AMR][1000 genomes]
rs10955180	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10955181	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10955184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10955185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11781352	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11985382	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11994001	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12056323	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12541026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12542022	1.00[CEU][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12542931	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12544768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12548477	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];0.99[ASN][1000 genomes]
rs12549563	0.84[EUR][1000 genomes]
rs12550198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs12677171	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13268777	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13270534	0.82[CHB][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16892236	1.00[CEU][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16897061	0.96[CEU][hapmap];0.83[JPT][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1893884	0.83[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes]
rs2001728	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34580087	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3802198	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4130753	0.81[CEU][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4236853	0.83[EUR][1000 genomes]
rs4301421	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4332102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4348458	0.80[EUR][1000 genomes]
rs4370499	0.96[CEU][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4388428	0.81[CEU][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4407850	0.82[EUR][1000 genomes]
rs4442112	0.83[JPT][hapmap]
rs4618666	0.87[EUR][1000 genomes]
rs4734406	0.81[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4734407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4735564	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4995528	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62532757	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6651181	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6985600	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6991043	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs7007360	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7011763	0.83[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes]
rs7015739	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7016626	0.83[JPT][hapmap]
rs7815227	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7845395	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7845750	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9642951	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027362	chr8:99469281-99715845	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv539689	chr8:99469281-99715845	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv891218	chr8:99507313-99906221	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv891219	chr8:99526819-99643487	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12547922	NACAP1	cis	parietal	SCAN
rs12547922	OSR2	cis	cerebellum	SCAN
rs12547922	PABPC1	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99490400-99547600	Weak transcription	Ovary	ovary
2	chr8:99500400-99558800	Weak transcription	Aorta	Aorta
3	chr8:99515000-99550800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr8:99516000-99542800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr8:99516200-99543000	Weak transcription	GM12878-XiMat	blood
6	chr8:99516800-99542800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr8:99518400-99542800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr8:99518800-99551000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr8:99519000-99543000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr8:99519000-99548400	Weak transcription	Fetal Stomach	stomach
11	chr8:99525800-99576400	Weak transcription	Pancreas	Pancrea
12	chr8:99526000-99543200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr8:99526200-99549400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr8:99531000-99569600	Weak transcription	HMEC	breast
15	chr8:99531200-99561800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr8:99531400-99543200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr8:99531400-99586400	Weak transcription	HSMM	muscle
18	chr8:99531600-99542800	Weak transcription	Fetal Kidney	kidney
19	chr8:99531600-99561800	Weak transcription	Esophagus	oesophagus
20	chr8:99532000-99542600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr8:99532000-99543000	Weak transcription	Fetal Muscle Leg	muscle
22	chr8:99532000-99543600	Weak transcription	Psoas Muscle	Psoas
23	chr8:99532000-99548000	Weak transcription	HSMMtube	muscle
24	chr8:99533400-99543000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr8:99533400-99566400	Weak transcription	NHLF	lung
26	chr8:99533600-99542800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr8:99533600-99543000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr8:99534600-99567200	Weak transcription	A549	lung
29	chr8:99534800-99543000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr8:99534800-99543600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr8:99534800-99549800	Weak transcription	Colon Smooth Muscle	Colon
32	chr8:99535000-99543000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr8:99535400-99571600	Weak transcription	Gastric	stomach
34	chr8:99536200-99542400	Weak transcription	Hela-S3	cervix
35	chr8:99536200-99543000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr8:99536600-99542600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr8:99536600-99543200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr8:99536800-99545000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr8:99537000-99542600	Weak transcription	Primary hematopoietic stem cells	blood
40	chr8:99537200-99542600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr8:99537600-99542600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr8:99537600-99542600	Weak transcription	Left Ventricle	heart
43	chr8:99537600-99543000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr8:99537600-99543000	Weak transcription	Adipose Nuclei	Adipose
45	chr8:99537600-99543000	Weak transcription	Fetal Intestine Large	intestine
46	chr8:99537600-99543400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr8:99537600-99543400	Weak transcription	Fetal Lung	lung
48	chr8:99537800-99543200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr8:99539000-99543200	Weak transcription	Dnd41	blood
50	chr8:99539000-99543600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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