Variant report

Variant	rs2852193
Chromosome Location	chr11:108429204-108429205
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:108422629..108424538-chr11:108427034..108429329,2	K562	blood:
2	chr11:108428359..108430191-chr11:108435380..108437514,2	K562	blood:
3	chr11:108421413..108424228-chr11:108426338..108429813,4	K562	blood:
4	chr11:108425445..108426959-chr11:108428665..108430478,2	K562	blood:

Variant related genes	Relation type
ENSG00000110723	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1940211	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1940212	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2155441	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2186783	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2256083	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2256362	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2256372	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2640753	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2640755	0.83[EUR][1000 genomes]
rs2640756	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2640757	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2640758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2640773	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2640774	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2846423	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2852189	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2852192	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2852194	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2852195	0.93[ASN][1000 genomes]
rs2852196	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4278482	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs767663	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs767664	0.91[AMR][1000 genomes];0.93[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
rs2852193	KDELC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 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	chr11:108423200-108429600	Weak transcription	NHLF	lung
5	chr11:108423400-108430000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr11:108423400-108432200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:108423400-108432400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr11:108423400-108436000	Weak transcription	Liver	Liver
9	chr11:108423600-108441400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:108423800-108432200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:108424200-108439400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr11:108425200-108430600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr11:108426400-108432600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:108427400-108429400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr11:108427800-108430800	Enhancers	GM12878-XiMat	blood
16	chr11:108427800-108432200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr11:108428400-108429800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:108428400-108429800	Weak transcription	Placenta	Placenta
19	chr11:108428600-108442000	Weak transcription	K562	blood
20	chr11:108429000-108430400	Strong transcription	NHEK	skin
21	chr11:108429000-108431000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr11:108429000-108432400	Enhancers	HSMMtube	muscle
23	chr11:108429200-108430000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr11:108429200-108430200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:108429200-108430400	Genic enhancers	Placenta Amnion	Placenta Amnion
26	chr11:108429200-108430800	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr11:108429200-108430800	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr11:108429200-108434600	Enhancers	HSMM	muscle

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