Variant report

Variant	rs17590006
Chromosome Location	chr1:85789270-85789271
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10493764	0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs11161618	1.00[YRI][hapmap]
rs11583836	1.00[YRI][hapmap]
rs12402128	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13373844	0.82[CHD][hapmap]
rs1523993	0.88[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[ASN][1000 genomes]
rs17123650	1.00[YRI][hapmap]
rs17387935	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35092233	0.88[ASN][1000 genomes]
rs35294786	0.86[ASN][1000 genomes]
rs35876501	0.86[ASN][1000 genomes]
rs35956189	0.83[ASN][1000 genomes]
rs36062892	0.97[ASN][1000 genomes]
rs3768226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61769484	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61769490	0.90[ASN][1000 genomes]
rs61783046	0.86[ASN][1000 genomes]
rs6659486	0.86[ASN][1000 genomes]
rs6669293	0.98[ASN][1000 genomes]
rs6673833	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs7540393	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]

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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17590006	ZNHIT6	cis	cerebellum	SCAN
rs17590006	BCL10	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85774600-85794800	Weak transcription	Spleen	Spleen
2	chr1:85774800-85790400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:85774800-85790600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr1:85774800-85794200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:85778200-85790400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:85778800-85789600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:85780000-85791800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:85780000-85795800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:85780200-85790400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:85780200-85795800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:85780400-85791600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:85780400-85793200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:85780400-85795800	Weak transcription	Gastric	stomach
14	chr1:85781800-85792800	Weak transcription	Pancreas	Pancrea
15	chr1:85782200-85790600	Genic enhancers	Muscle Satellite Cultured Cells	--
16	chr1:85782400-85795000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:85782800-85794600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:85783000-85795800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:85783200-85795800	Weak transcription	Aorta	Aorta
20	chr1:85783800-85789800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:85783800-85791000	Genic enhancers	Osteobl	bone
22	chr1:85784000-85789600	Strong transcription	HepG2	liver
23	chr1:85784000-85790400	Weak transcription	Left Ventricle	heart
24	chr1:85784000-85794600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:85784600-85794600	Weak transcription	Fetal Lung	lung
26	chr1:85784800-85789400	Genic enhancers	HSMM	muscle
27	chr1:85785200-85789400	Strong transcription	Liver	Liver
28	chr1:85785800-85789400	Genic enhancers	NHDF-Ad	bronchial
29	chr1:85785800-85789600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:85785800-85789800	Strong transcription	Fetal Intestine Large	intestine
31	chr1:85786200-85789400	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:85786200-85790400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:85786400-85791200	Strong transcription	Fetal Intestine Small	intestine
34	chr1:85786600-85789400	Enhancers	NH-A	brain
35	chr1:85786600-85790000	Weak transcription	Fetal Heart	heart
36	chr1:85786600-85790400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:85786600-85790600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:85786600-85791400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:85786600-85791600	Weak transcription	Fetal Kidney	kidney
40	chr1:85786800-85790400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:85787200-85789400	Weak transcription	Lung	lung
42	chr1:85787200-85790600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:85787200-85793600	Weak transcription	HSMMtube	muscle
44	chr1:85787400-85790400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:85787400-85790600	Weak transcription	Hela-S3	cervix
46	chr1:85787400-85791600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr1:85787600-85789400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:85787600-85789400	Strong transcription	Fetal Muscle Leg	muscle
49	chr1:85787600-85790800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:85787600-85791000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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