Variant report

Variant	rs12544621
Chromosome Location	chr8:125543936-125543937
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:125487117..125490518-chr8:125542261..125547751,5	K562	blood:
2	chr8:125543795..125545961-chr8:125826867..125829379,2	K562	blood:
3	chr8:125542543..125545366-chr8:125564681..125567341,2	MCF-7	breast:
4	chr8:125543458..125545211-chr8:125571140..125573606,2	MCF-7	breast:
5	chr8:125482386..125490832-chr8:125532319..125553620,55	MCF-7	breast:
6	chr8:125543036..125544991-chr8:125560441..125563068,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255491	Chromatin interaction
ENSG00000170881	Chromatin interaction
ENSG00000245149	Chromatin interaction
ENSG00000147684	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10956184	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10956185	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10956189	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12542260	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12544211	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12545267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12546906	0.85[AMR][1000 genomes]
rs12548836	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12550707	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12550827	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];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28576577	1.00[LWK][hapmap]
rs4512366	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4551335	0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4602869	0.85[AMR][1000 genomes]
rs5004281	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56942034	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57941917	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62527883	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62527886	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62527901	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62527908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62527910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6987213	0.81[AMR][1000 genomes]
rs6987358	0.83[AMR][1000 genomes]
rs7009847	0.81[AMR][1000 genomes]
rs7830325	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7845008	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531508	chr8:125390194-125587953	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12544621	TRMT12	cis	multi-tissue	Pritchard
rs12544621	ZHX2	cis	parietal	SCAN
rs12544621	ZHX2	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125488200-125550400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:125496600-125549600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr8:125496800-125547400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr8:125500000-125549600	Weak transcription	Fetal Brain Male	brain
5	chr8:125501600-125550000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr8:125504000-125550800	Weak transcription	Spleen	Spleen
7	chr8:125516200-125549600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr8:125516200-125549600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr8:125516400-125549600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr8:125519200-125550000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr8:125520000-125550600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr8:125525200-125549600	Weak transcription	Brain Germinal Matrix	brain
13	chr8:125527600-125550200	Weak transcription	Fetal Brain Female	brain
14	chr8:125528000-125550400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr8:125529200-125544000	Weak transcription	Fetal Stomach	stomach
16	chr8:125531400-125547400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr8:125531400-125550000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr8:125531600-125544200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr8:125531600-125548400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr8:125531600-125550000	Weak transcription	Fetal Lung	lung
21	chr8:125532000-125544000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr8:125532200-125544000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr8:125535800-125550000	Weak transcription	Thymus	Thymus
24	chr8:125537200-125544000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr8:125537200-125544400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr8:125537200-125550400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr8:125537800-125550400	Weak transcription	Esophagus	oesophagus
28	chr8:125538000-125544200	Enhancers	Fetal Intestine Small	intestine
29	chr8:125538200-125549600	Weak transcription	HUVEC	blood vessel
30	chr8:125538400-125544400	Enhancers	Fetal Intestine Large	intestine
31	chr8:125538400-125544400	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr8:125538400-125545000	Weak transcription	Ovary	ovary
33	chr8:125538400-125549800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr8:125539000-125549400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr8:125539400-125545000	Weak transcription	NHLF	lung
36	chr8:125539400-125549800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr8:125539600-125544000	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr8:125539600-125549600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr8:125539800-125549000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr8:125539800-125550200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr8:125540000-125545000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr8:125540000-125550000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr8:125540200-125544400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr8:125540200-125549400	Weak transcription	HMEC	breast
45	chr8:125540200-125549600	Weak transcription	HSMMtube	muscle
46	chr8:125540200-125549600	Weak transcription	Osteobl	bone
47	chr8:125540200-125549800	Weak transcription	NHDF-Ad	bronchial
48	chr8:125540200-125550000	Weak transcription	NH-A	brain
49	chr8:125540200-125550200	Weak transcription	Fetal Kidney	kidney
50	chr8:125540200-125550600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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