Variant report

Variant	rs11739347
Chromosome Location	chr5:112516435-112516436
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1007172	0.80[JPT][hapmap];0.86[AMR][1000 genomes]
rs10072487	0.84[JPT][hapmap]
rs13153785	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs1345078	0.85[CEU][hapmap];0.85[TSI][hapmap]
rs1348431	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs2044241	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs2416313	0.85[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.84[ASN][1000 genomes]
rs2416314	0.81[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[ASN][1000 genomes]
rs2416315	0.84[JPT][hapmap]
rs2900071	0.90[CEU][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs4705801	0.84[CEU][hapmap]
rs4705802	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs6859190	0.80[JPT][hapmap]
rs6876116	0.84[JPT][hapmap];0.81[MEX][hapmap]
rs6896522	0.84[CHB][hapmap];0.80[JPT][hapmap];0.90[AMR][1000 genomes]
rs7719681	0.85[TSI][hapmap]
rs935163	0.85[CEU][hapmap];0.85[TSI][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11739347	TSSK1B	cis	cerebellum	SCAN
rs11739347	WDR36	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112500800-112518400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:112504800-112525600	Weak transcription	Esophagus	oesophagus
3	chr5:112505800-112521400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:112506200-112518200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:112506400-112521600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:112507000-112526000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:112512600-112521400	Weak transcription	Brain Angular Gyrus	brain
8	chr5:112512800-112518400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:112513000-112521400	Weak transcription	NHEK	skin
10	chr5:112513800-112517000	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr5:112514200-112518600	Weak transcription	Right Atrium	heart
12	chr5:112514400-112530600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr5:112515000-112522200	Weak transcription	Adipose Nuclei	Adipose
14	chr5:112515200-112521600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr5:112515200-112526400	Weak transcription	Lung	lung
16	chr5:112515400-112521400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:112515600-112517600	Weak transcription	Ovary	ovary
18	chr5:112515600-112518800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:112515600-112519200	Enhancers	Fetal Heart	heart
20	chr5:112515600-112519400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr5:112515600-112521000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:112515600-112521400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr5:112515600-112521800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr5:112515600-112521800	Weak transcription	Liver	Liver
25	chr5:112515800-112517400	Weak transcription	Left Ventricle	heart
26	chr5:112515800-112521000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr5:112515800-112521800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr5:112515800-112530200	Weak transcription	Psoas Muscle	Psoas
29	chr5:112515800-112538000	Weak transcription	Fetal Kidney	kidney
30	chr5:112516000-112518400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr5:112516000-112521200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr5:112516000-112521400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:112516000-112521800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr5:112516200-112517600	Weak transcription	Right Ventricle	heart
35	chr5:112516200-112518000	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:112516200-112521000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:112516400-112524000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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