Variant report

Variant	rs17158194
Chromosome Location	chr15:83544584-83544585
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83416895..83419331-chr15:83542514..83545188,2	K562	blood:
2	chr15:83543732..83546327-chr15:83548068..83551024,3	K562	blood:
3	chr15:83540274..83544098-chr15:83544468..83546572,4	K562	blood:

Variant related genes	Relation type
ENSG00000250988	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1002881	0.88[JPT][hapmap];0.84[MEX][hapmap]
rs1108135	0.84[MKK][hapmap]
rs11259954	0.86[CEU][hapmap];0.82[JPT][hapmap]
rs12101624	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1256424	0.88[JPT][hapmap]
rs1256426	0.94[JPT][hapmap]
rs12592976	0.84[MKK][hapmap]
rs1588546	0.93[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[ASN][1000 genomes]
rs17158132	0.81[GIH][hapmap]
rs17158168	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17158267	0.87[MKK][hapmap]
rs17841162	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17841163	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17841165	0.84[MKK][hapmap]
rs2127648	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2306428	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2667377	0.83[JPT][hapmap]
rs2667378	0.88[JPT][hapmap]
rs28698473	0.84[AFR][1000 genomes]
rs3784365	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3784366	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs56108482	0.84[AFR][1000 genomes]
rs56686717	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7174216	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7174726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8030940	0.87[ASW][hapmap];0.88[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17158194	TM6SF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83504600-83549400	Weak transcription	Psoas Muscle	Psoas
2	chr15:83520000-83549800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr15:83520000-83563800	Weak transcription	Brain Hippocampus Middle	brain
4	chr15:83520200-83547000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:83523600-83558000	Weak transcription	Esophagus	oesophagus
6	chr15:83524600-83567800	Weak transcription	Left Ventricle	heart
7	chr15:83524800-83563800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr15:83537000-83551400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr15:83538000-83549600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr15:83540200-83545400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:83540400-83544600	Weak transcription	HepG2	liver
12	chr15:83540600-83573200	Weak transcription	Right Atrium	heart
13	chr15:83540800-83563600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:83541000-83566200	Weak transcription	Spleen	Spleen
15	chr15:83541200-83545600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:83541600-83545000	Weak transcription	Colon Smooth Muscle	Colon
17	chr15:83542200-83544600	Weak transcription	Fetal Brain Female	brain
18	chr15:83542400-83551000	Weak transcription	Right Ventricle	heart
19	chr15:83542400-83564000	Weak transcription	Lung	lung
20	chr15:83542400-83567200	Weak transcription	Brain Angular Gyrus	brain
21	chr15:83542800-83558000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:83543000-83557600	Weak transcription	Fetal Stomach	stomach
23	chr15:83543400-83545000	Genic enhancers	Pancreas	Pancrea
24	chr15:83543400-83545200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:83543600-83545000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:83543600-83545000	Enhancers	Muscle Satellite Cultured Cells	--
27	chr15:83543600-83545000	Enhancers	HSMM	muscle
28	chr15:83543600-83557800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr15:83543600-83558000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:83543600-83567600	Weak transcription	Aorta	Aorta
31	chr15:83543800-83544800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr15:83543800-83544800	Enhancers	NHDF-Ad	bronchial
33	chr15:83544000-83544600	Enhancers	HSMMtube	muscle
34	chr15:83544000-83544800	Enhancers	NHEK	skin
35	chr15:83544000-83545000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:83544000-83545000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:83544000-83545000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:83544000-83545000	Enhancers	HMEC	breast
39	chr15:83544000-83545000	Enhancers	NH-A	brain
40	chr15:83544000-83545000	Enhancers	Osteobl	bone
41	chr15:83544000-83550800	Weak transcription	Gastric	stomach
42	chr15:83544000-83551000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr15:83544000-83558000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr15:83544000-83558000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr15:83544000-83563800	Weak transcription	Brain Anterior Caudate	brain
46	chr15:83544200-83544800	Enhancers	NHLF	lung
47	chr15:83544200-83545000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr15:83544200-83545000	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr15:83544200-83546400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr15:83544200-83549000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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