Variant report

Variant	rs2140420
Chromosome Location	chr6:35064041-35064042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:35060379..35062413-chr6:35062564..35064850,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs2005	0.82[JPT][hapmap]
rs2395609	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2494096	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2689097	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2762341	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2762342	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2762350	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2820229	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];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777748	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6920194	0.81[ASN][1000 genomes]
rs707967	0.88[CEU][hapmap];0.81[MKK][hapmap];0.86[EUR][1000 genomes]
rs707968	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7772251	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs820078	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs820079	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs820080	0.81[EUR][1000 genomes]
rs820081	0.81[EUR][1000 genomes]
rs820084	0.81[CEU][hapmap]
rs820086	0.81[CEU][hapmap]
rs820089	0.81[CEU][hapmap]
rs820094	0.81[CEU][hapmap]
rs820097	0.81[CEU][hapmap]
rs9348964	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.86[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	nsv869750	chr6:35031548-35085585	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2140420	ANKS1A	cis	parietal	SCAN
rs2140420	ANKS1A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35053400-35064200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:35056600-35064200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr6:35058000-35064200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:35060600-35064200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:35060600-35064600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:35060800-35065000	Weak transcription	Left Ventricle	heart
7	chr6:35061000-35064200	Weak transcription	Fetal Lung	lung
8	chr6:35062000-35064200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:35062000-35064200	Weak transcription	Adipose Nuclei	Adipose
10	chr6:35062800-35065000	Enhancers	Osteobl	bone
11	chr6:35063000-35064600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr6:35063000-35064800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr6:35063000-35065000	Enhancers	Hela-S3	cervix
14	chr6:35063200-35064800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:35063200-35064800	Enhancers	HepG2	liver
16	chr6:35063200-35065000	Enhancers	NHDF-Ad	bronchial
17	chr6:35063200-35065200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:35063400-35064200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:35063400-35064600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:35063400-35064600	Enhancers	Brain Anterior Caudate	brain
21	chr6:35063400-35064600	Enhancers	Brain Substantia Nigra	brain
22	chr6:35063400-35064800	Enhancers	Liver	Liver
23	chr6:35063400-35065000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:35063400-35065000	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr6:35063400-35065000	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr6:35063400-35065800	Enhancers	Brain Germinal Matrix	brain
27	chr6:35063600-35064200	Enhancers	NHLF	lung
28	chr6:35063600-35064400	Enhancers	Rectal Smooth Muscle	rectum
29	chr6:35063600-35064600	Enhancers	Brain Hippocampus Middle	brain
30	chr6:35063600-35064600	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr6:35063600-35064600	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr6:35063600-35064600	Enhancers	Stomach Smooth Muscle	stomach
33	chr6:35063600-35064800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:35063600-35064800	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr6:35063600-35065000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:35063600-35065000	Enhancers	Muscle Satellite Cultured Cells	--
37	chr6:35063600-35065400	Enhancers	Fetal Stomach	stomach
38	chr6:35063600-35065600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:35063600-35065600	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr6:35063600-35065600	Enhancers	NH-A	brain
41	chr6:35063800-35064200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:35063800-35064400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:35063800-35064400	Enhancers	Duodenum Mucosa	Duodenum
44	chr6:35063800-35064600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:35063800-35064600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:35063800-35064600	Enhancers	Brain Angular Gyrus	brain
47	chr6:35063800-35064600	Enhancers	Brain Cingulate Gyrus	brain
48	chr6:35063800-35064600	Enhancers	Ovary	ovary
49	chr6:35063800-35064800	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr6:35063800-35064800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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