Variant report

Variant	rs6594687
Chromosome Location	chr5:112464987-112464988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10037489	0.82[ASN][1000 genomes]
rs10040328	0.82[ASN][1000 genomes]
rs10519336	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[ASN][1000 genomes]
rs13156718	0.84[CEU][hapmap]
rs13186032	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1443689	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2165929	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2900067	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3922563	0.96[CEU][hapmap];0.81[TSI][hapmap]
rs3922583	0.96[CEU][hapmap]
rs3922584	0.91[CEU][hapmap]
rs4078252	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4078253	0.96[CEU][hapmap];0.83[TSI][hapmap]
rs4078254	0.96[CEU][hapmap];0.81[TSI][hapmap]
rs4705543	0.84[CEU][hapmap]
rs4705544	0.95[CEU][hapmap]
rs4705780	0.96[CEU][hapmap];0.83[TSI][hapmap]
rs4705782	0.81[TSI][hapmap]
rs4705783	1.00[CEU][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs6594683	0.96[CEU][hapmap];0.83[TSI][hapmap]
rs6594686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6859611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6860460	0.86[CHB][hapmap]
rs7702177	0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[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	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6594687	SRP19	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112451000-112478800	Weak transcription	Aorta	Aorta
2	chr5:112456600-112467200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:112458400-112474200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:112458600-112474000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:112458600-112477000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:112458800-112476600	Weak transcription	NHEK	skin
7	chr5:112459400-112468400	Weak transcription	NHDF-Ad	bronchial
8	chr5:112460600-112465000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr5:112460800-112466800	Weak transcription	Fetal Brain Male	brain
10	chr5:112460800-112467400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:112461000-112466600	Weak transcription	Right Atrium	heart
12	chr5:112461200-112469400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr5:112461400-112466200	Weak transcription	Left Ventricle	heart
14	chr5:112461400-112466600	Weak transcription	Right Ventricle	heart
15	chr5:112461400-112468400	Weak transcription	Ovary	ovary
16	chr5:112461400-112476800	Weak transcription	Fetal Muscle Leg	muscle
17	chr5:112461800-112476200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:112462000-112467400	Weak transcription	Adipose Nuclei	Adipose
19	chr5:112462200-112466600	Weak transcription	Fetal Heart	heart
20	chr5:112462200-112475600	Weak transcription	Liver	Liver
21	chr5:112462400-112465200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr5:112462400-112466200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:112462600-112476200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr5:112462800-112465200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:112463600-112465000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:112463600-112465200	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr5:112464600-112465000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr5:112464600-112465000	Enhancers	Psoas Muscle	Psoas
29	chr5:112464600-112465200	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr5:112464600-112468200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr5:112464800-112465000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:112464800-112467200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr5:112464800-112468200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr5:112464800-112470000	Weak transcription	Fetal Brain Female	brain
35	chr5:112464800-112476800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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