Variant report

Variant	rs591917
Chromosome Location	chr1:85905136-85905137
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10782548	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1146382	0.91[CHB][hapmap]
rs1146384	0.85[EUR][1000 genomes]
rs11587876	0.84[CHD][hapmap]
rs233046	0.95[CEU][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs233051	0.81[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs233080	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs233111	0.90[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap]
rs233128	0.90[CEU][hapmap]
rs2474123	0.86[CHB][hapmap]
rs34278923	0.81[ASN][1000 genomes]
rs648216	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7532508	1.00[CEU][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[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	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs591917	PKN2	cis	parietal	SCAN
rs591917	C1orf180	cis	parietal	SCAN
rs591917	MCOLN3	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85886400-85914200	Weak transcription	HSMMtube	muscle
2	chr1:85892200-85906200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:85893800-85906200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:85893800-85916800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:85899200-85914800	Weak transcription	Esophagus	oesophagus
6	chr1:85901400-85923000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:85902400-85905200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr1:85902400-85905200	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr1:85902400-85905400	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr1:85902400-85906200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:85902600-85912200	Weak transcription	Pancreas	Pancrea
12	chr1:85902800-85905400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr1:85903000-85906000	Weak transcription	Ovary	ovary
14	chr1:85903000-85906800	Weak transcription	Lung	lung
15	chr1:85903400-85907000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:85903600-85905200	Enhancers	Fetal Kidney	kidney
17	chr1:85903600-85906600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:85903600-85906800	Enhancers	Adipose Nuclei	Adipose
19	chr1:85903600-85907000	Enhancers	HepG2	liver
20	chr1:85903600-85907200	Enhancers	Muscle Satellite Cultured Cells	--
21	chr1:85903600-85907200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:85903600-85907600	Enhancers	NHDF-Ad	bronchial
23	chr1:85903800-85906800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:85903800-85906800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:85903800-85907200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:85903800-85907400	Enhancers	HUVEC	blood vessel
27	chr1:85903800-85907400	Enhancers	NHLF	lung
28	chr1:85903800-85907400	Enhancers	Osteobl	bone
29	chr1:85904200-85905400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:85904200-85905400	Enhancers	Fetal Lung	lung
31	chr1:85904200-85906000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:85904200-85906800	Enhancers	NH-A	brain
33	chr1:85904400-85906600	Weak transcription	Psoas Muscle	Psoas
34	chr1:85904400-85906600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:85904400-85907000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:85904400-85914800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:85904600-85910200	Weak transcription	Fetal Intestine Large	intestine
38	chr1:85904800-85905200	Enhancers	Fetal Muscle Leg	muscle
39	chr1:85904800-85905200	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr1:85904800-85905200	Enhancers	Small Intestine	intestine
41	chr1:85904800-85906600	Enhancers	HSMM	muscle
42	chr1:85904800-85907200	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr1:85905000-85905200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:85905000-85905200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:85905000-85905200	Enhancers	Duodenum Mucosa	Duodenum
46	chr1:85905000-85905200	Enhancers	Fetal Stomach	stomach
47	chr1:85905000-85905200	Enhancers	Left Ventricle	heart
48	chr1:85905000-85905200	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr1:85905000-85905200	Enhancers	Stomach Smooth Muscle	stomach
50	chr1:85905000-85906400	Weak transcription	Liver	Liver

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