Variant report

Variant	rs11599962
Chromosome Location	chr11:108434421-108434422
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10890853	0.83[AMR][1000 genomes]
rs10890858	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11212695	0.83[AMR][1000 genomes]
rs17092330	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17092334	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1940219	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2155437	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2846407	0.91[ASN][1000 genomes]
rs3741060	0.91[AMR][1000 genomes]
rs4442514	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4533001	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4754325	0.91[AMR][1000 genomes];0.81[EUR][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	nsv1052254	chr11:108122683-108845008	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv541164	chr11:108122683-108845008	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv898386	chr11:108409442-108831875	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11599962	KDELC2	Cis_1M	lymphoblastoid	RTeQTL
rs11599962	KDELC2	cis	Heart Left Ventricle	GTEx
rs11599962	KDELC2	cis	Artery Tibial	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108417200-108441400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:108422400-108441600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr11:108423000-108436000	Weak transcription	Fetal Intestine Small	intestine
4	chr11:108423400-108436000	Weak transcription	Liver	Liver
5	chr11:108423600-108441400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr11:108424200-108439400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr11:108428600-108442000	Weak transcription	K562	blood
8	chr11:108429200-108434600	Enhancers	HSMM	muscle
9	chr11:108430400-108436600	Weak transcription	Brain Hippocampus Middle	brain
10	chr11:108431000-108434600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:108431000-108436200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr11:108432200-108434600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:108432200-108434600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr11:108432200-108434800	Genic enhancers	Placenta	Placenta
15	chr11:108432200-108435200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:108432600-108434600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:108432800-108434600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr11:108432800-108434600	Enhancers	NHDF-Ad	bronchial
19	chr11:108432800-108436200	Weak transcription	Lung	lung
20	chr11:108432800-108438200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr11:108432800-108438600	Weak transcription	Pancreas	Pancrea
22	chr11:108432800-108441200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr11:108432800-108441600	Weak transcription	HMEC	breast
24	chr11:108433000-108434600	Enhancers	HSMMtube	muscle
25	chr11:108433000-108444000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr11:108433200-108434600	Enhancers	Placenta Amnion	Placenta Amnion
27	chr11:108433600-108434600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr11:108433600-108434600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:108433600-108434600	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr11:108433800-108434600	Enhancers	Psoas Muscle	Psoas
31	chr11:108434000-108434600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:108434000-108434600	Enhancers	Gastric	stomach
33	chr11:108434200-108434600	Enhancers	Esophagus	oesophagus
34	chr11:108434200-108434800	Strong transcription	NHEK	skin
35	chr11:108434400-108437600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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