Variant report

Variant	rs12023231
Chromosome Location	chr1:149989434-149989435
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:149853005..149861438-chr1:149978765..149991065,34	MCF-7	breast:
2	chr1:149906356..149909616-chr1:149987905..149990846,3	MCF-7	breast:
3	chr1:149988147..149991518-chr1:149991864..149994674,3	K562	blood:
4	chr1:149988828..149991415-chr1:150020920..150022808,2	MCF-7	breast:
5	chr1:149864943..149867381-chr1:149988938..149991665,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184678	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000014914	Chromatin interaction
ENSG00000178096	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10494260	1.00[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes]
rs11205309	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11205310	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs11205312	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12022928	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12026500	0.85[AMR][1000 genomes]
rs12409885	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1868992	0.89[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap]
rs3738320	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs3767627	1.00[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes]
rs3767628	0.89[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs3936952	0.83[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap]
rs4926386	0.92[GIH][hapmap];0.86[JPT][hapmap]
rs4926400	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes]
rs57252299	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58700306	0.98[ASN][1000 genomes]
rs61584789	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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	nsv831537	chr1:149833357-150064655	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	431 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12023231	TCHHL1	cis	parietal	SCAN
rs12023231	SCNM1	cis	parietal	SCAN
rs12023231	VPS72	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:149982800-149994400	Weak transcription	Gastric	stomach
2	chr1:149983000-149992800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:149985000-149989600	Weak transcription	Colonic Mucosa	Colon
4	chr1:149985000-149993200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:149985200-149993200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:149985400-149989600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:149985400-149990200	Weak transcription	Brain Anterior Caudate	brain
8	chr1:149985400-149993000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:149985600-149994000	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:149985600-150022000	Weak transcription	Brain Substantia Nigra	brain
11	chr1:149986200-149990400	Enhancers	Placenta	Placenta
12	chr1:149987400-149989800	Enhancers	Placenta Amnion	Placenta Amnion
13	chr1:149988000-149993200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:149988200-149992800	Weak transcription	Adipose Nuclei	Adipose
15	chr1:149988200-149992800	Weak transcription	A549	lung
16	chr1:149988200-149993200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:149988200-149993200	Weak transcription	Osteobl	bone
18	chr1:149988400-149993200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:149988800-149989800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr1:149988800-149990000	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr1:149988800-149991000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:149989000-149989600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:149989000-149990000	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr1:149989000-149990000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:149989000-149990600	Enhancers	Stomach Mucosa	stomach
26	chr1:149989000-149991000	Enhancers	Fetal Intestine Small	intestine
27	chr1:149989200-149989600	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr1:149989200-149989800	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr1:149989200-149989800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:149989200-149989800	Enhancers	HMEC	breast
31	chr1:149989200-149989800	Enhancers	NHEK	skin
32	chr1:149989200-149990000	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr1:149989200-149990400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr1:149989200-149990800	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr1:149989400-149989600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:149989400-149989600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:149989400-149989600	Enhancers	K562	blood
38	chr1:149989400-149989800	Enhancers	Left Ventricle	heart
39	chr1:149989400-149989800	Enhancers	Pancreas	Pancrea
40	chr1:149989400-149989800	Enhancers	GM12878-XiMat	blood
41	chr1:149989400-149990000	Enhancers	Fetal Intestine Large	intestine
42	chr1:149989400-149990000	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr1:149989400-149990000	Enhancers	Hela-S3	cervix
44	chr1:149989400-149991200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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