Variant report

Variant	rs11637422
Chromosome Location	chr15:40860709-40860710
allele	A/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	MXI1	chr15:40860597-40862522	SK-N-SH	brain:	n/a	n/a
2	HCFC1	chr15:40860574-40863139	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
RPUSD2	TF binding region
C15orf57	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10152546	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1044474	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10518697	0.92[EUR][1000 genomes]
rs1058734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070283	0.91[EUR][1000 genomes]
rs11630273	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11633184	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11637245	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12324748	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12385982	0.91[EUR][1000 genomes]
rs12441754	0.83[EUR][1000 genomes]
rs12903817	0.87[EUR][1000 genomes]
rs12908316	0.89[EUR][1000 genomes]
rs12913296	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12913739	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12915171	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12915636	0.92[EUR][1000 genomes]
rs13329076	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17673703	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17674454	0.91[EUR][1000 genomes]
rs17747423	0.92[EUR][1000 genomes]
rs17747633	0.92[EUR][1000 genomes]
rs1814541	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1814542	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2412525	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28634695	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28647196	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28669075	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34739056	0.82[EUR][1000 genomes]
rs34824658	0.88[EUR][1000 genomes]
rs35127391	0.92[EUR][1000 genomes]
rs35684277	0.86[EUR][1000 genomes]
rs35842610	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4923880	0.90[EUR][1000 genomes]
rs4924486	0.90[EUR][1000 genomes]
rs62019876	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62019879	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71471880	0.86[EUR][1000 genomes]
rs7165509	0.86[EUR][1000 genomes]
rs7170288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175747	0.85[EUR][1000 genomes]
rs8029530	0.82[EUR][1000 genomes]
rs8036891	0.82[EUR][1000 genomes]
rs8037180	0.84[EUR][1000 genomes]
rs8038122	0.86[EUR][1000 genomes]
rs8042386	0.84[EUR][1000 genomes]
rs9920642	0.86[EUR][1000 genomes]
rs9920676	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs11637422	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs11637422	RP11-111A22.1	cis	Stomach	GTEx
rs11637422	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs11637422	CCDC32	cis	multi-tissue	Pritchard
rs11637422	C15orf57	cis	Esophagus Muscularis	GTEx
rs11637422	RP11-111A22.1	cis	Artery Tibial	GTEx
rs11637422	C15orf57	cis	Heart Left Ventricle	GTEx
rs11637422	RAD51	cis	multi-tissue	Pritchard
rs11637422	C15orf57	cis	Artery Aorta	GTEx
rs11637422	RP11-111A22.1	cis	lung	GTEx
rs11637422	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs11637422	C15orf57	cis	Stomach	GTEx
rs11637422	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs11637422	C15orf57	cis	Muscle Skeletal	GTEx
rs11637422	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs11637422	C15orf57	cis	Esophagus Mucosa	GTEx
rs11637422	C15orf57	cis	Artery Tibial	GTEx
rs11637422	C15orf57	cis	Nerve Tibial	GTEx
rs11637422	C15orf57	cis	lung	GTEx
rs11637422	RP11-111A22.1	cis	Artery Aorta	GTEx
rs11637422	C15orf57	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40857200-40861200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:40857400-40860800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:40857600-40860800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:40857800-40860800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:40857800-40860800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:40857800-40860800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:40857800-40860800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr15:40857800-40860800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr15:40857800-40860800	Weak transcription	Colon Smooth Muscle	Colon
10	chr15:40857800-40860800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr15:40857800-40860800	Weak transcription	Fetal Lung	lung
12	chr15:40857800-40860800	Weak transcription	Stomach Mucosa	stomach
13	chr15:40857800-40860800	Weak transcription	NHLF	lung
14	chr15:40857800-40860800	Weak transcription	Osteobl	bone
15	chr15:40857800-40861000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:40857800-40861000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:40857800-40861000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:40857800-40861000	Weak transcription	HSMM	muscle
19	chr15:40857800-40861000	Weak transcription	HSMMtube	muscle
20	chr15:40857800-40861200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr15:40857800-40861200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:40858000-40860800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:40858000-40860800	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr15:40858000-40860800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr15:40858000-40860800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr15:40858000-40860800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr15:40858000-40860800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr15:40858000-40860800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr15:40858000-40860800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr15:40858000-40860800	Weak transcription	Adipose Nuclei	Adipose
31	chr15:40858000-40860800	Weak transcription	Colonic Mucosa	Colon
32	chr15:40858000-40860800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr15:40858000-40860800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr15:40858000-40860800	Weak transcription	Fetal Stomach	stomach
35	chr15:40858000-40860800	Weak transcription	NHEK	skin
36	chr15:40858000-40861000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr15:40858000-40861000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr15:40858000-40861000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:40858000-40861000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr15:40858000-40861000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr15:40858000-40861000	Weak transcription	Right Ventricle	heart
42	chr15:40858000-40861200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr15:40858000-40861200	Weak transcription	Lung	lung
44	chr15:40858000-40861200	Weak transcription	Pancreas	Pancrea
45	chr15:40858000-40861400	Weak transcription	Spleen	Spleen
46	chr15:40858200-40860800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr15:40858200-40860800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr15:40858200-40861000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr15:40858400-40860800	Weak transcription	Fetal Heart	heart
50	chr15:40858800-40860800	Weak transcription	Placenta	Placenta

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