Variant report

Variant	rs12086463
Chromosome Location	chr1:226790197-226790198
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226789700..226791399-chr1:226794121..226795784,2	K562	blood:
2	chr1:226789700..226792954-chr1:226793236..226797673,6	K562	blood:
3	chr1:226789996..226792506-chr1:227056884..227059360,2	MCF-7	breast:
4	chr1:226770710..226772918-chr1:226790123..226792228,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143801	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10799362	0.86[CHD][hapmap]
rs10916011	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10916012	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12035052	0.81[MEX][hapmap]
rs12086425	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3738717	0.94[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3820632	0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs4653758	0.84[EUR][1000 genomes]
rs497911	0.81[MEX][hapmap]
rs6663978	0.86[CHD][hapmap]
rs6664080	0.86[CHD][hapmap]
rs6667555	0.86[CHD][hapmap]
rs6697883	0.83[CHD][hapmap]
rs7512486	0.86[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[ASN][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	nsv470779	chr1:226778432-226833304	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv873234	chr1:226779449-226859676	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv3437833	chr1:226780025-226810577	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv522446	chr1:226785530-226923938	Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12086463	DNAH14	cis	parietal	SCAN
rs12086463	DUSP5P	cis	parietal	SCAN
rs12086463	ACBD3	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226774800-226790200	Weak transcription	Fetal Intestine Small	intestine
2	chr1:226778800-226790400	Weak transcription	Fetal Brain Female	brain
3	chr1:226784000-226790200	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:226785200-226790200	Weak transcription	Brain Anterior Caudate	brain
5	chr1:226789200-226790600	Enhancers	Stomach Smooth Muscle	stomach
6	chr1:226789200-226790800	Enhancers	Fetal Muscle Leg	muscle
7	chr1:226789200-226792400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:226789200-226792400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:226789400-226790200	Weak transcription	Spleen	Spleen
10	chr1:226789400-226791000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr1:226789400-226791600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:226789600-226790200	Enhancers	NHDF-Ad	bronchial
13	chr1:226789600-226790200	Enhancers	NHLF	lung
14	chr1:226789600-226790600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:226789600-226790800	Enhancers	Fetal Brain Male	brain
16	chr1:226789600-226791600	Enhancers	Small Intestine	intestine
17	chr1:226789600-226792000	Enhancers	HMEC	breast
18	chr1:226789600-226793000	Enhancers	Brain Germinal Matrix	brain
19	chr1:226789600-226793000	Enhancers	Fetal Stomach	stomach
20	chr1:226789600-226795200	Enhancers	Placenta Amnion	Placenta Amnion
21	chr1:226789800-226790200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:226789800-226790400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:226789800-226790400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr1:226789800-226791800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:226789800-226792800	Enhancers	Fetal Lung	lung
26	chr1:226789800-226793400	Enhancers	HSMMtube	muscle
27	chr1:226789800-226795600	Enhancers	Placenta	Placenta
28	chr1:226790000-226790200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:226790000-226790200	Enhancers	Muscle Satellite Cultured Cells	--
30	chr1:226790000-226790200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:226790000-226790200	Enhancers	Osteobl	bone
32	chr1:226790000-226790400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:226790000-226790400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:226790000-226790400	Enhancers	Fetal Thymus	thymus
35	chr1:226790000-226790400	Genic enhancers	Right Atrium	heart
36	chr1:226790000-226790600	Enhancers	Brain Hippocampus Middle	brain
37	chr1:226790000-226790600	Enhancers	Colonic Mucosa	Colon
38	chr1:226790000-226790600	Enhancers	Esophagus	oesophagus
39	chr1:226790000-226790600	Enhancers	Lung	lung
40	chr1:226790000-226790600	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr1:226790000-226790600	Enhancers	NHEK	skin
42	chr1:226790000-226790800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:226790000-226790800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:226790000-226790800	Enhancers	Adipose Nuclei	Adipose
45	chr1:226790000-226790800	Enhancers	Brain Substantia Nigra	brain
46	chr1:226790000-226790800	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr1:226790000-226790800	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr1:226790000-226790800	Enhancers	Stomach Mucosa	stomach
49	chr1:226790000-226790800	Enhancers	HSMM	muscle
50	chr1:226790000-226791600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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