Variant report

Variant	rs10890859
Chromosome Location	chr11:108422872-108422873
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:108422127..108426041-chr11:108463043..108466411,3	K562	blood:

Variant related genes	Relation type
ENSG00000110723	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10749920	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs10789666	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs10890851	0.86[EUR][1000 genomes]
rs10890852	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs10890853	0.91[CEU][hapmap]
rs10890855	0.85[EUR][1000 genomes]
rs10890858	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11212682	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11212689	0.86[EUR][1000 genomes]
rs11212691	0.86[EUR][1000 genomes]
rs11212700	0.92[CEU][hapmap]
rs11212704	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11824250	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs12362341	0.85[EUR][1000 genomes]
rs17092330	0.91[CEU][hapmap]
rs1940212	0.93[JPT][hapmap]
rs1940219	0.91[CEU][hapmap]
rs2016291	0.95[EUR][1000 genomes]
rs2155437	0.93[ASN][1000 genomes]
rs2846407	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs2852189	0.93[JPT][hapmap]
rs3741060	0.83[CEU][hapmap]
rs3900699	0.83[EUR][1000 genomes]
rs4278482	0.94[JPT][hapmap]
rs4442514	0.91[CEU][hapmap];0.82[JPT][hapmap]
rs4533001	0.91[CEU][hapmap];0.82[JPT][hapmap]
rs4643041	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4753844	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs4754326	0.86[EUR][1000 genomes]
rs7104503	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7118229	0.85[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10890859	KDELC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108409200-108423000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr11:108417200-108441400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:108419600-108423400	Enhancers	Liver	Liver
4	chr11:108420000-108424000	Enhancers	Placenta	Placenta
5	chr11:108420800-108423000	Enhancers	Lung	lung
6	chr11:108420800-108423800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:108420800-108427600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr11:108421800-108423200	Flanking Active TSS	HSMMtube	muscle
9	chr11:108422000-108423000	Active TSS	NHDF-Ad	bronchial
10	chr11:108422000-108423400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:108422000-108423600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr11:108422200-108423000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr11:108422200-108423200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:108422200-108423200	Enhancers	Muscle Satellite Cultured Cells	--
15	chr11:108422200-108423400	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr11:108422200-108423600	Enhancers	Stomach Mucosa	stomach
17	chr11:108422200-108423600	Flanking Active TSS	K562	blood
18	chr11:108422200-108424200	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr11:108422400-108423000	Enhancers	H1 Cell Line	embryonic stem cell
20	chr11:108422400-108423000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr11:108422400-108423000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr11:108422400-108423000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:108422400-108423000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:108422400-108423000	Enhancers	Esophagus	oesophagus
25	chr11:108422400-108423200	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr11:108422400-108423200	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr11:108422400-108423200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:108422400-108423200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr11:108422400-108423400	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr11:108422400-108423400	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr11:108422400-108423400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr11:108422400-108441600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr11:108422600-108423000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:108422600-108423000	Flanking Active TSS	Fetal Kidney	kidney
35	chr11:108422600-108423400	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr11:108422600-108423600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:108422600-108423600	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr11:108422800-108423000	Enhancers	H9 Cell Line	embryonic stem cell
39	chr11:108422800-108423000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr11:108422800-108423000	Enhancers	Fetal Intestine Small	intestine
41	chr11:108422800-108423000	Active TSS	NHLF	lung
42	chr11:108422800-108423400	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr11:108422800-108423400	Enhancers	NHEK	skin
44	chr11:108422800-108425800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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