Variant report

Variant	rs883509
Chromosome Location	chr4:99563676-99563677
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	chr4:99551429..99553596-chr4:99563119..99565613,2	K562	blood:
2	chr4:99548903..99550666-chr4:99562029..99564226,2	K562	blood:

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10489126	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10516435	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17027883	0.96[ASN][1000 genomes]
rs17027886	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs41399047	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6829297	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6831674	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7685150	0.92[ASN][1000 genomes]
rs7699492	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs883510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv594940	chr4:99542475-99573350	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs883509	ADH1A	cis	cerebellum	SCAN
rs883509	ADH5	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99548000-99569200	Weak transcription	Gastric	stomach
2	chr4:99548000-99577000	Weak transcription	Esophagus	oesophagus
3	chr4:99552600-99569600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:99552800-99569200	Weak transcription	Fetal Stomach	stomach
5	chr4:99553200-99564200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:99554000-99564000	Weak transcription	Osteobl	bone
7	chr4:99554200-99564200	Weak transcription	Pancreas	Pancrea
8	chr4:99554200-99569200	Weak transcription	Spleen	Spleen
9	chr4:99554400-99564200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:99558200-99564200	Weak transcription	Fetal Heart	heart
11	chr4:99559400-99564400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:99560200-99565600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:99560200-99569200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:99560600-99564200	Weak transcription	Thymus	Thymus
15	chr4:99560600-99568000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr4:99560800-99564200	Weak transcription	Fetal Thymus	thymus
17	chr4:99560800-99566400	Weak transcription	Brain Germinal Matrix	brain
18	chr4:99560800-99568200	Weak transcription	Fetal Lung	lung
19	chr4:99561000-99564800	Weak transcription	Primary T cells from cord blood	blood
20	chr4:99561000-99566000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr4:99561200-99564800	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr4:99561200-99565200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:99561200-99565400	Enhancers	NHDF-Ad	bronchial
24	chr4:99561200-99567000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr4:99561200-99567200	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr4:99561600-99564400	Weak transcription	Fetal Brain Female	brain
27	chr4:99561600-99564800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:99561600-99564800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr4:99562000-99564200	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr4:99562000-99564400	Weak transcription	Ovary	ovary
31	chr4:99562000-99565000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr4:99562000-99566000	Enhancers	Muscle Satellite Cultured Cells	--
33	chr4:99562000-99569200	Weak transcription	Fetal Brain Male	brain
34	chr4:99562200-99564200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr4:99562600-99564200	Enhancers	NH-A	brain
36	chr4:99562600-99564800	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr4:99562600-99565000	Enhancers	Brain Hippocampus Middle	brain
38	chr4:99562600-99565200	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr4:99562800-99563800	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr4:99562800-99564600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:99562800-99564800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:99563000-99563800	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr4:99563000-99564200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr4:99563000-99564400	Weak transcription	Brain Anterior Caudate	brain
45	chr4:99563000-99565200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr4:99563200-99564200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:99563200-99564200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr4:99563200-99564200	Weak transcription	NHLF	lung
49	chr4:99563200-99564800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr4:99563200-99565200	Enhancers	HMEC	breast

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