Variant report

Variant	rs4924687
Chromosome Location	chr15:42860591-42860592
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:42860282-42863171	K562	blood:	n/a	n/a
2	POLR2A	chr15:42860370-42860894	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr15:42860468-42860918	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42854171..42864590-chr15:42864872..42869799,12	K562	blood:
2	chr15:42854080..42855765-chr15:42858958..42860703,2	K562	blood:

Variant related genes	Relation type
ENSG00000260490	TF binding region
ENSG00000159433	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10518766	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1060291	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1060293	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851410	1.00[CHB][hapmap];0.83[GIH][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];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs16973320	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17709180	1.00[ASN][1000 genomes]
rs17709377	1.00[ASN][1000 genomes]
rs17766532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1900921	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2412709	0.82[CEU][hapmap]
rs2899051	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2899059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs34359922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34643746	1.00[ASN][1000 genomes]
rs34792942	1.00[ASN][1000 genomes]
rs3986280	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4923948	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4924684	1.00[ASN][1000 genomes]
rs56357092	1.00[ASN][1000 genomes]
rs56982416	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58042601	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58641431	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59697584	1.00[ASN][1000 genomes]
rs59705032	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60380503	1.00[ASN][1000 genomes]
rs60584955	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60812675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61489160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022317	1.00[ASN][1000 genomes]
rs7180483	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73402783	1.00[ASN][1000 genomes]
rs73402785	1.00[ASN][1000 genomes]
rs73404714	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73404717	0.80[EUR][1000 genomes]
rs73404723	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73404730	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73404763	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73406518	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73406534	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73406545	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];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]

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	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4924687	LRRC57	cis	multi-tissue	Pritchard
rs4924687	LRRC57	cis	Esophagus Muscularis	GTEx
rs4924687	LRRC57	Cis_1M	lymphoblastoid	RTeQTL
rs4924687	LRRC57	cis	Liver	GTEx
rs4924687	CEP27	Cis_1M	lymphoblastoid	RTeQTL
rs4924687	XM_063823	cis	multi-tissue	Pritchard
rs4924687	LRRC57	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42841600-42866800	Weak transcription	Stomach Mucosa	stomach
2	chr15:42841800-42867000	Weak transcription	Ovary	ovary
3	chr15:42842200-42867000	Weak transcription	Psoas Muscle	Psoas
4	chr15:42842400-42867000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:42842600-42867400	Weak transcription	Small Intestine	intestine
6	chr15:42842800-42867000	Weak transcription	Fetal Kidney	kidney
7	chr15:42843000-42863000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:42848000-42861400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:42848600-42861200	Strong transcription	Fetal Intestine Large	intestine
10	chr15:42849200-42861400	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr15:42849400-42866800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:42849800-42861000	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr15:42849800-42861200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:42849800-42861200	Strong transcription	GM12878-XiMat	blood
15	chr15:42849800-42862800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr15:42850000-42861400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr15:42850000-42862800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr15:42850200-42861000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:42850200-42861200	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr15:42850200-42861200	Strong transcription	Primary T cells from cord blood	blood
21	chr15:42850400-42861200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:42850400-42861200	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:42850600-42860600	Strong transcription	Fetal Intestine Small	intestine
24	chr15:42850600-42861200	Strong transcription	Fetal Thymus	thymus
25	chr15:42850800-42861000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:42850800-42861000	Strong transcription	Brain Germinal Matrix	brain
27	chr15:42850800-42861000	Strong transcription	Fetal Muscle Trunk	muscle
28	chr15:42850800-42861200	Strong transcription	Duodenum Mucosa	Duodenum
29	chr15:42850800-42861400	Strong transcription	Adipose Nuclei	Adipose
30	chr15:42851000-42861000	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr15:42851000-42861200	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr15:42851000-42861200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:42851000-42861200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr15:42851000-42861400	Strong transcription	Liver	Liver
35	chr15:42851000-42861800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:42851200-42860800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr15:42851200-42861000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr15:42851400-42860600	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr15:42851400-42862800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr15:42851600-42861200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr15:42851600-42866600	Weak transcription	Fetal Heart	heart
42	chr15:42852000-42867000	Weak transcription	Colonic Mucosa	Colon
43	chr15:42853400-42861000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr15:42853400-42861800	Strong transcription	Fetal Brain Female	brain
45	chr15:42853800-42860600	Strong transcription	Fetal Stomach	stomach
46	chr15:42854000-42861000	Strong transcription	Lung	lung
47	chr15:42854200-42867000	Weak transcription	HSMMtube	muscle
48	chr15:42854400-42861200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr15:42854800-42867000	Weak transcription	Pancreas	Pancrea
50	chr15:42855000-42864400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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