Variant report

Variant	rs1940219
Chromosome Location	chr11:108430554-108430555
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10749920	0.84[CEU][hapmap]
rs10789666	0.84[CEU][hapmap]
rs10890852	0.84[CEU][hapmap]
rs10890853	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs10890858	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10890859	0.91[CEU][hapmap]
rs11212682	0.84[CEU][hapmap]
rs11212695	0.86[AMR][1000 genomes]
rs11212700	0.84[CEU][hapmap]
rs11212704	0.91[CEU][hapmap];0.83[JPT][hapmap]
rs11599962	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11824250	0.84[CEU][hapmap]
rs17092330	1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17092334	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2155437	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2846407	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs3741060	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4442514	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4533001	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4753844	0.84[CEU][hapmap]
rs4754325	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7104503	0.91[CEU][hapmap]

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
rs1940219	KDELC2	cis	Artery Tibial	GTEx
rs1940219	KDELC2	cis	Heart Left Ventricle	GTEx
rs1940219	KDELC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

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	chr11:108423400-108432200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr11:108423400-108432400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr11:108423400-108436000	Weak transcription	Liver	Liver
7	chr11:108423600-108441400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr11:108423800-108432200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:108424200-108439400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr11:108425200-108430600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:108426400-108432600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr11:108427800-108430800	Enhancers	GM12878-XiMat	blood
13	chr11:108427800-108432200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr11:108428600-108442000	Weak transcription	K562	blood
15	chr11:108429000-108431000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr11:108429000-108432400	Enhancers	HSMMtube	muscle
17	chr11:108429200-108430800	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr11:108429200-108430800	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr11:108429200-108434600	Enhancers	HSMM	muscle
20	chr11:108429400-108431000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr11:108429400-108431000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr11:108429600-108431000	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr11:108429600-108431000	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr11:108429600-108431200	Enhancers	HMEC	breast
25	chr11:108429600-108432200	Weak transcription	Aorta	Aorta
26	chr11:108429800-108430600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr11:108429800-108430600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:108429800-108430600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:108429800-108430800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:108429800-108431200	Enhancers	Adipose Nuclei	Adipose
31	chr11:108430000-108430600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr11:108430000-108430800	Flanking Active TSS	NHDF-Ad	bronchial
33	chr11:108430000-108431000	Enhancers	Primary T cells from cord blood	blood
34	chr11:108430000-108431000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr11:108430000-108431200	Enhancers	Fetal Lung	lung
36	chr11:108430000-108432400	Enhancers	NH-A	brain
37	chr11:108430200-108430600	Weak transcription	Placenta	Placenta
38	chr11:108430200-108430800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr11:108430200-108430800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr11:108430200-108431000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr11:108430200-108431000	Flanking Active TSS	Osteobl	bone
42	chr11:108430200-108431200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr11:108430200-108431400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr11:108430400-108430600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr11:108430400-108430600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr11:108430400-108430600	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr11:108430400-108430800	Genic enhancers	NHEK	skin
48	chr11:108430400-108430800	Active TSS	NHLF	lung
49	chr11:108430400-108431200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr11:108430400-108431600	Enhancers	Fetal Kidney	kidney

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