Variant report

Variant	rs11955699
Chromosome Location	chr5:112498949-112498950
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112492439..112494935-chr5:112498208..112500030,2	K562	blood:
2	chr5:112492254..112496189-chr5:112498530..112504608,6	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10072487	0.83[CEU][hapmap]
rs13156236	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13159159	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13159631	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1443685	1.00[CEU][hapmap];0.84[CHD][hapmap];0.92[LWK][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1443687	0.87[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2165933	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2416315	0.83[CEU][hapmap]
rs4705547	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705801	0.80[EUR][1000 genomes]
rs6859190	0.82[CEU][hapmap]
rs7703089	0.86[EUR][1000 genomes]
rs7719681	0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs7720516	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7733404	0.82[TSI][hapmap]
rs935162	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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
rs11955699	TSSK1B	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112477400-112500600	Weak transcription	Fetal Stomach	stomach
2	chr5:112486800-112500400	Weak transcription	Gastric	stomach
3	chr5:112489200-112500000	Weak transcription	Liver	Liver
4	chr5:112493200-112499800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:112493200-112500400	Weak transcription	Aorta	Aorta
6	chr5:112493800-112500400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:112493800-112504600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:112494800-112500400	Weak transcription	Lung	lung
9	chr5:112494800-112500600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:112495800-112506400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:112496000-112502400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr5:112496000-112506000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:112496200-112501800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr5:112496200-112502200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr5:112496400-112501800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr5:112496400-112502400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:112496600-112501600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr5:112496800-112503000	Enhancers	HMEC	breast
19	chr5:112497000-112499200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr5:112497000-112500200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr5:112497200-112499200	Flanking Active TSS	NHEK	skin
22	chr5:112497200-112501200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr5:112497400-112499200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:112497600-112499000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr5:112497600-112499200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:112497600-112499200	Enhancers	Right Atrium	heart
27	chr5:112497600-112499400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:112497600-112501600	Enhancers	Right Ventricle	heart
29	chr5:112497600-112503600	Enhancers	Ovary	ovary
30	chr5:112497800-112499800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr5:112497800-112500000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr5:112497800-112503800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr5:112497800-112504400	Weak transcription	Fetal Muscle Leg	muscle
34	chr5:112498000-112503600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:112498200-112499000	Enhancers	Psoas Muscle	Psoas
36	chr5:112498200-112499000	Enhancers	Stomach Mucosa	stomach
37	chr5:112498200-112499200	Enhancers	Left Ventricle	heart
38	chr5:112498200-112499400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr5:112498200-112499400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:112498200-112499400	Enhancers	NHDF-Ad	bronchial
41	chr5:112498200-112500800	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr5:112498200-112502000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr5:112498400-112499000	Enhancers	Hela-S3	cervix
44	chr5:112498400-112499200	Enhancers	Muscle Satellite Cultured Cells	--
45	chr5:112498400-112499400	Enhancers	Adipose Nuclei	Adipose
46	chr5:112498400-112499400	Enhancers	NHLF	lung
47	chr5:112498400-112499600	Enhancers	Osteobl	bone
48	chr5:112498400-112500600	Weak transcription	Placenta	Placenta
49	chr5:112498400-112502000	Enhancers	NH-A	brain
50	chr5:112498400-112502400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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