Variant report

Variant	rs12542931
Chromosome Location	chr8:99548896-99548897
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:99548500..99551679-chr8:99552322..99555998,3	K562	blood:
2	chr8:99547855..99550787-chr8:99555161..99557416,2	MCF-7	breast:
3	chr8:99548557..99552364-chr8:99553180..99556021,3	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10086870	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10098835	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10099978	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10100346	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10100378	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10100577	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10101919	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10108828	0.86[JPT][hapmap]
rs10111264	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10441501	0.83[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10955174	0.81[EUR][1000 genomes]
rs10955175	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10955176	0.82[ASW][hapmap];0.95[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10955177	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10955179	0.82[JPT][hapmap]
rs10955180	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10955181	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[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];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11781352	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[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];0.89[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11994001	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12056323	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.82[LWK][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.87[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];0.86[LWK][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12542022	1.00[CEU][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12544768	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]
rs12547922	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]
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[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];0.97[ASN][1000 genomes]
rs12549563	0.83[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];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12677171	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13268777	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13270534	0.82[CHB][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];0.83[TSI][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16892236	1.00[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs16897061	0.95[CEU][hapmap];0.83[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1893884	0.83[JPT][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes]
rs2001728	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34580087	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3802198	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4130753	0.83[JPT][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4236853	0.82[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];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4332102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4348458	0.81[EUR][1000 genomes]
rs4370499	0.95[CEU][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4388428	0.83[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4407850	0.82[EUR][1000 genomes]
rs4442112	0.83[JPT][hapmap]
rs4618666	0.88[EUR][1000 genomes]
rs4734406	0.90[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4734407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4735564	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.82[LWK][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4995528	0.90[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62532757	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6651181	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6985600	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6991043	0.86[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs7007360	0.90[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7011763	0.83[JPT][hapmap];0.89[TSI][hapmap];0.84[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];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7016626	0.83[JPT][hapmap]
rs7815227	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[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];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7845750	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9642951	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv611808	chr8:99544765-99591736	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	nsv1030498	chr8:99545493-99607093	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99500400-99558800	Weak transcription	Aorta	Aorta
2	chr8:99515000-99550800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr8:99518800-99551000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr8:99525800-99576400	Weak transcription	Pancreas	Pancrea
5	chr8:99526200-99549400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr8:99531000-99569600	Weak transcription	HMEC	breast
7	chr8:99531200-99561800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr8:99531400-99586400	Weak transcription	HSMM	muscle
9	chr8:99531600-99561800	Weak transcription	Esophagus	oesophagus
10	chr8:99533400-99566400	Weak transcription	NHLF	lung
11	chr8:99534600-99567200	Weak transcription	A549	lung
12	chr8:99534800-99549800	Weak transcription	Colon Smooth Muscle	Colon
13	chr8:99535400-99571600	Weak transcription	Gastric	stomach
14	chr8:99539200-99553000	Weak transcription	HepG2	liver
15	chr8:99543000-99566800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr8:99543600-99553200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr8:99543800-99555000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr8:99544000-99552400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr8:99544000-99552400	Weak transcription	Placenta	Placenta
20	chr8:99544000-99552800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr8:99544000-99559000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr8:99544000-99560800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr8:99544000-99566800	Weak transcription	Brain Substantia Nigra	brain
24	chr8:99544200-99552200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr8:99544200-99558800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr8:99544200-99559400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr8:99544600-99549600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr8:99544600-99556000	Weak transcription	Left Ventricle	heart
29	chr8:99544600-99560000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr8:99544600-99587000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr8:99544800-99551000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr8:99544800-99553600	Weak transcription	Fetal Intestine Large	intestine
33	chr8:99544800-99554800	Weak transcription	Lung	lung
34	chr8:99545000-99553200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr8:99545000-99553800	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr8:99545000-99554200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr8:99545000-99554800	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr8:99545200-99552400	Weak transcription	GM12878-XiMat	blood
39	chr8:99545400-99552200	Weak transcription	Dnd41	blood
40	chr8:99545400-99552600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr8:99545600-99553400	Weak transcription	NHEK	skin
42	chr8:99546000-99552600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr8:99546000-99571600	Weak transcription	Fetal Intestine Small	intestine
44	chr8:99546400-99553000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr8:99546400-99557000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr8:99546600-99552400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr8:99546600-99555600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr8:99546600-99576400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr8:99547600-99549600	Enhancers	Osteobl	bone
50	chr8:99547600-99550400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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