Variant report

Variant	rs6570726
Chromosome Location	chr6:146159460-146159461
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:146134408..146136747-chr6:146158257..146160540,2	MCF-7	breast:
2	chr6:146131042..146132915-chr6:146157627..146159920,2	K562	blood:
3	chr6:146054185..146056773-chr6:146157994..146159853,2	K562	blood:
4	chr6:146158963..146161449-chr6:146161903..146164839,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FBXO30-1	chr6:146159314-146160471	l_3286_chr6:146156330-146160471_brain

Variant related genes	Relation type
ENSG00000112425	Chromatin interaction
ENSG00000118496	Chromatin interaction
ENSG00000270638	Chromatin interaction
ENSG00000235652	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1004752	0.82[CEU][hapmap]
rs1011596	0.82[CEU][hapmap]
rs1011597	0.81[CEU][hapmap]
rs10872579	0.81[CEU][hapmap]
rs11961703	0.81[YRI][hapmap]
rs1292333	0.82[CEU][hapmap]
rs1292334	0.82[CEU][hapmap]
rs1292335	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs1292336	0.82[CEU][hapmap]
rs1292337	0.82[CEU][hapmap]
rs1292339	0.89[CEU][hapmap]
rs1337839	0.82[CEU][hapmap]
rs1337840	0.81[EUR][1000 genomes]
rs1337841	0.82[CEU][hapmap]
rs1415744	0.82[CEU][hapmap]
rs17075280	0.88[YRI][hapmap]
rs17075537	0.88[YRI][hapmap]
rs1856244	0.88[YRI][hapmap]
rs1883365	0.82[CEU][hapmap]
rs1890171	0.82[CEU][hapmap]
rs1935617	0.80[EUR][1000 genomes]
rs2050027	0.82[CEU][hapmap]
rs2092263	0.82[CEU][hapmap]
rs2247317	0.81[CEU][hapmap]
rs2247571	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2253648	0.85[CEU][hapmap]
rs2265477	0.81[CEU][hapmap];0.81[GIH][hapmap]
rs2328704	0.89[CEU][hapmap]
rs2777475	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2814864	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs4075695	0.81[CEU][hapmap]
rs4243478	0.81[CEU][hapmap]
rs4895683	0.81[CEU][hapmap]
rs4896831	0.89[CEU][hapmap]
rs4896832	0.82[CEU][hapmap]
rs4896833	0.82[CEU][hapmap]
rs4896838	0.82[CEU][hapmap]
rs4896851	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6570705	0.82[CEU][hapmap]
rs6570723	0.81[CEU][hapmap]
rs6930154	0.85[CEU][hapmap]
rs6930181	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs702313	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7739735	0.82[CEU][hapmap]
rs7740785	0.84[EUR][1000 genomes]
rs7744014	0.82[CEU][hapmap]
rs7753770	0.82[CEU][hapmap]
rs857875	0.82[CEU][hapmap]
rs857877	0.82[CEU][hapmap]
rs857879	0.82[CEU][hapmap]
rs857880	0.82[CEU][hapmap]
rs857882	0.82[CEU][hapmap]
rs857883	0.82[CEU][hapmap]
rs868721	0.88[YRI][hapmap]
rs9373473	0.85[EUR][1000 genomes]
rs9373476	0.82[CEU][hapmap]
rs9376957	0.82[CEU][hapmap]
rs9376961	0.82[CEU][hapmap]
rs9390343	0.88[CEU][hapmap]
rs9390344	0.92[CEU][hapmap]
rs9390357	0.82[CEU][hapmap]
rs9399568	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9403737	0.82[CEU][hapmap]
rs9403739	0.82[CEU][hapmap]
rs9403741	0.82[CEU][hapmap]
rs9403742	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs9485018	0.81[CEU][hapmap]
rs9497395	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034226	chr6:146071068-146306942	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv830835	chr6:146145148-146287473	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6570726	EPM2A	cis	parietal	SCAN
rs6570726	SHPRH	cis	cerebellum	SCAN
rs6570726	SHPRH	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146136800-146165200	Weak transcription	Lung	lung
2	chr6:146137400-146167200	Weak transcription	Primary B cells from cord blood	blood
3	chr6:146137800-146159600	Weak transcription	Psoas Muscle	Psoas
4	chr6:146137800-146163000	Weak transcription	Fetal Stomach	stomach
5	chr6:146150600-146163000	Weak transcription	Left Ventricle	heart
6	chr6:146150600-146171200	Weak transcription	Aorta	Aorta
7	chr6:146150600-146174000	Weak transcription	Right Ventricle	heart
8	chr6:146157600-146163200	Weak transcription	Brain Germinal Matrix	brain
9	chr6:146157800-146162800	Weak transcription	Gastric	stomach
10	chr6:146158000-146163400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr6:146158200-146159600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:146158200-146163600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:146158200-146163600	Weak transcription	HSMMtube	muscle
14	chr6:146158200-146163600	Weak transcription	Osteobl	bone
15	chr6:146158200-146164200	Weak transcription	Brain Anterior Caudate	brain
16	chr6:146158200-146166000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr6:146158400-146163600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:146158800-146159600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:146158800-146159600	Enhancers	Placenta	Placenta
20	chr6:146158800-146159800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:146158800-146160000	Enhancers	Placenta Amnion	Placenta Amnion
22	chr6:146158800-146160000	Enhancers	NHEK	skin
23	chr6:146159000-146159600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:146159000-146160000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:146159000-146160000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:146159000-146160200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:146159200-146159800	Enhancers	Hela-S3	cervix
28	chr6:146159200-146160000	Enhancers	HMEC	breast
29	chr6:146159200-146160600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:146159200-146162400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr6:146159400-146159600	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr6:146159400-146159800	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr6:146159400-146159800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:146159400-146159800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:146159400-146159800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:146159400-146159800	Enhancers	NHDF-Ad	bronchial

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