Variant report

Variant	rs11631690
Chromosome Location	chr15:76519136-76519137
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:76517181..76519721-chr15:76602211..76604425,2	K562	blood:

Variant related genes	Relation type
ENSG00000140374	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11072576	0.85[EUR][1000 genomes]
rs11072577	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11072578	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11072579	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11072583	0.80[EUR][1000 genomes]
rs11072585	0.81[EUR][1000 genomes]
rs11072587	0.81[EUR][1000 genomes]
rs11629459	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11631764	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11631874	0.81[EUR][1000 genomes]
rs11634472	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11636851	0.87[EUR][1000 genomes]
rs11637855	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12050896	0.81[EUR][1000 genomes]
rs1850722	0.81[EUR][1000 genomes]
rs1875888	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2007928	0.85[EUR][1000 genomes]
rs2016734	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2404974	0.81[EUR][1000 genomes]
rs2456050	0.85[EUR][1000 genomes]
rs2456057	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2456071	0.80[EUR][1000 genomes]
rs2469548	0.87[EUR][1000 genomes]
rs3784449	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3898352	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4592616	0.85[EUR][1000 genomes]
rs4886777	0.81[EUR][1000 genomes]
rs4886779	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4886781	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886783	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4886784	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4886787	0.87[EUR][1000 genomes]
rs4886789	0.81[EUR][1000 genomes]
rs5012144	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55805818	0.81[EUR][1000 genomes]
rs56737606	0.81[EUR][1000 genomes]
rs57182285	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60017340	0.81[EUR][1000 genomes]
rs60290059	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60371615	0.85[EUR][1000 genomes]
rs61275737	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61300240	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62030232	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6495197	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7177923	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8033494	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8039063	0.81[EUR][1000 genomes]
rs870295	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs879625	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs883993	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs937732	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs937733	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569998	chr15:76232605-76550938	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv833057	chr15:76367848-76585868	ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11631690	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs11631690	RP11-593F23.1	cis	Skin Sun Exposed Lower leg	GTEx
rs11631690	SCAPER	cis	Whole Blood	GTEx
rs11631690	SCAPER	cis	Thyroid	GTEx
rs11631690	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs11631690	SCAPER	cis	lung	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76489400-76519800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr15:76492800-76526400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr15:76493600-76526400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr15:76499200-76527400	Weak transcription	Fetal Brain Male	brain
5	chr15:76500600-76534800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr15:76501200-76524200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:76503600-76551400	Weak transcription	Small Intestine	intestine
8	chr15:76506000-76526800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:76506200-76526800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr15:76506400-76525600	Weak transcription	Fetal Brain Female	brain
11	chr15:76507200-76551400	Weak transcription	Brain Hippocampus Middle	brain
12	chr15:76508000-76525000	Weak transcription	NHLF	lung
13	chr15:76508000-76525400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr15:76508200-76521400	Weak transcription	NHDF-Ad	bronchial
15	chr15:76508400-76546000	Weak transcription	Brain Anterior Caudate	brain
16	chr15:76508600-76525200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr15:76510000-76523000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr15:76510000-76534600	Weak transcription	Brain Substantia Nigra	brain
19	chr15:76510200-76526000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr15:76510200-76555400	Weak transcription	Psoas Muscle	Psoas
21	chr15:76510400-76523600	Weak transcription	HMEC	breast
22	chr15:76510400-76538000	Weak transcription	HUVEC	blood vessel
23	chr15:76510400-76538200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:76510400-76555000	Weak transcription	NH-A	brain
25	chr15:76511800-76525400	Strong transcription	Liver	Liver
26	chr15:76512000-76525400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr15:76512000-76525600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr15:76513200-76559400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr15:76513400-76524800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:76513600-76522400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:76513600-76523800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr15:76513800-76551400	Weak transcription	Stomach Mucosa	stomach
33	chr15:76514200-76525000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr15:76514800-76520000	Strong transcription	Fetal Intestine Small	intestine
35	chr15:76514800-76525000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr15:76515200-76523800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:76515800-76523600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr15:76516000-76520800	Strong transcription	HepG2	liver
39	chr15:76516400-76550600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr15:76517200-76551800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:76517400-76519600	Weak transcription	Gastric	stomach
42	chr15:76517400-76521600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr15:76517400-76523000	Weak transcription	Lung	lung
44	chr15:76517400-76532600	Weak transcription	HSMM	muscle
45	chr15:76517400-76544600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr15:76517400-76549200	Weak transcription	Fetal Kidney	kidney
47	chr15:76517400-76550600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr15:76517400-76550600	Weak transcription	Pancreas	Pancrea
49	chr15:76517400-76559400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr15:76517600-76519400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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