Variant report

Variant	rs17709180
Chromosome Location	chr15:42746391-42746392
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42726730..42728462-chr15:42744444..42747241,2	K562	blood:

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10518763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs10518766	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1060291	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1060293	1.00[ASN][1000 genomes]
rs10851410	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11022	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11070376	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11636577	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12324717	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12594633	0.82[EUR][1000 genomes]
rs1659215	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs16973053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs16973059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs16973095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs16973107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs16973132	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs16973137	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs16973148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs16973153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973155	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs16973171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16973320	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17695121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs17709377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17766532	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1801449	0.82[CEU][hapmap]
rs1900921	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2412704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28364347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs28364348	0.83[EUR][1000 genomes]
rs2899051	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2899059	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34359922	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs34643746	1.00[ASN][1000 genomes]
rs34792942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3986280	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4344713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs4583208	0.85[CEU][hapmap]
rs4923948	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4924676	0.85[EUR][1000 genomes]
rs4924684	1.00[ASN][1000 genomes]
rs4924687	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs56357092	1.00[ASN][1000 genomes]
rs56982416	1.00[ASN][1000 genomes]
rs57134130	0.81[EUR][1000 genomes]
rs58042601	1.00[ASN][1000 genomes]
rs58641431	1.00[ASN][1000 genomes]
rs59697584	1.00[ASN][1000 genomes]
rs59705032	1.00[ASN][1000 genomes]
rs60380503	1.00[ASN][1000 genomes]
rs60584955	1.00[ASN][1000 genomes]
rs60812675	1.00[ASN][1000 genomes]
rs61489160	1.00[ASN][1000 genomes]
rs61753567	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62022317	1.00[ASN][1000 genomes]
rs7164437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs7164874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7165023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7178901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7180483	1.00[ASN][1000 genomes]
rs7182797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs73402783	1.00[ASN][1000 genomes]
rs73402785	1.00[ASN][1000 genomes]
rs73404714	1.00[ASN][1000 genomes]
rs73404723	1.00[ASN][1000 genomes]
rs73404730	1.00[ASN][1000 genomes]
rs73404763	1.00[ASN][1000 genomes]
rs73406518	1.00[ASN][1000 genomes]
rs73406534	1.00[ASN][1000 genomes]
rs73406545	1.00[ASN][1000 genomes]
rs74009095	1.00[ASN][1000 genomes]
rs8033412	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8037100	1.00[CEU][hapmap]
rs8038153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv832986	chr15:42587825-42753664	Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv832987	chr15:42627447-42792348	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	esv3334708	chr15:42664344-42827738	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17709180	LRRC57	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42694600-42750600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr15:42700800-42747200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr15:42701200-42766600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr15:42702200-42750200	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr15:42704000-42746800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:42705800-42749200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr15:42709800-42747000	Weak transcription	Stomach Mucosa	stomach
8	chr15:42711800-42749200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr15:42720400-42759200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr15:42721800-42747400	Strong transcription	HSMM	muscle
11	chr15:42730800-42746800	Strong transcription	Hela-S3	cervix
12	chr15:42733200-42747400	Strong transcription	Placenta	Placenta
13	chr15:42733400-42747000	Strong transcription	Primary B cells from peripheral blood	blood
14	chr15:42733400-42747200	Strong transcription	Primary B cells from cord blood	blood
15	chr15:42733400-42748000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:42737000-42747200	Strong transcription	Osteobl	bone
17	chr15:42737200-42764800	Weak transcription	A549	lung
18	chr15:42738400-42746600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:42738600-42747200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:42740800-42749200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr15:42741800-42747200	Strong transcription	Fetal Intestine Large	intestine
22	chr15:42742400-42746800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr15:42742400-42746800	Weak transcription	Right Atrium	heart
24	chr15:42742600-42749200	Weak transcription	Pancreas	Pancrea
25	chr15:42743200-42750200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr15:42743800-42749400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:42744000-42747000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr15:42744000-42747400	Weak transcription	Aorta	Aorta
29	chr15:42744000-42747800	Weak transcription	Psoas Muscle	Psoas
30	chr15:42744000-42748400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:42744000-42749000	Weak transcription	Brain Angular Gyrus	brain
32	chr15:42744000-42749200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:42744000-42749200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr15:42744000-42749200	Weak transcription	Esophagus	oesophagus
35	chr15:42744000-42757400	Weak transcription	Gastric	stomach
36	chr15:42744000-42757600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr15:42744200-42746400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr15:42744200-42746600	Strong transcription	Fetal Muscle Leg	muscle
39	chr15:42744200-42746600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr15:42744200-42746800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr15:42744200-42746800	Weak transcription	Colon Smooth Muscle	Colon
42	chr15:42744200-42746800	Weak transcription	Left Ventricle	heart
43	chr15:42744200-42747000	Weak transcription	Fetal Kidney	kidney
44	chr15:42744200-42747000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr15:42744200-42747800	Weak transcription	NHLF	lung
46	chr15:42744200-42748000	Weak transcription	Adipose Nuclei	Adipose
47	chr15:42744200-42748400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr15:42744200-42748400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr15:42744200-42748400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:42744200-42748600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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