Variant report

Variant	rs2252102
Chromosome Location	chr11:8998158-8998159
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8996657..8999652-chr11:9004082..9006608,2	MCF-7	breast:
2	chr11:8996724..8999605-chr11:9022687..9025353,2	K562	blood:

Variant related genes	Relation type
ENSG00000175352	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10219366	0.84[EUR][1000 genomes]
rs10769976	0.85[EUR][1000 genomes]
rs10840156	0.85[EUR][1000 genomes]
rs12785559	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12786377	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12790020	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12794962	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12798311	0.82[EUR][1000 genomes]
rs12805109	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1347016	0.89[ASN][1000 genomes]
rs1985026	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2016844	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2056903	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2116510	0.89[ASN][1000 genomes]
rs2116511	0.89[ASN][1000 genomes]
rs2246878	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2247038	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2316541	0.87[ASN][1000 genomes]
rs2568047	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2568069	0.89[ASN][1000 genomes]
rs2568074	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2568075	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2568077	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2568079	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2568081	0.87[ASN][1000 genomes]
rs2568086	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2568087	0.89[ASN][1000 genomes]
rs2568088	0.83[ASN][1000 genomes]
rs2653590	0.89[ASN][1000 genomes]
rs2653597	0.80[ASN][1000 genomes]
rs2653601	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2653604	0.89[ASN][1000 genomes]
rs2653611	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2742473	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742483	0.80[AMR][1000 genomes]
rs2742486	0.89[ASN][1000 genomes]
rs2742487	0.89[ASN][1000 genomes]
rs2742488	0.89[ASN][1000 genomes]
rs2742489	0.83[ASN][1000 genomes]
rs2742491	0.89[ASN][1000 genomes]
rs2742493	0.89[ASN][1000 genomes]
rs2742495	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2742496	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2742497	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2742504	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2742505	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2742512	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2742513	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2742514	0.83[ASN][1000 genomes]
rs3751063	0.85[EUR][1000 genomes]
rs4264185	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4370967	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4909951	0.85[EUR][1000 genomes]
rs4910181	0.81[EUR][1000 genomes]
rs4910313	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66630602	0.85[ASN][1000 genomes]
rs7124403	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72852790	0.87[ASN][1000 genomes]
rs72853712	0.87[ASN][1000 genomes]
rs7940895	0.90[ASN][1000 genomes]
rs909464	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9300096	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv896984	chr11:8988550-9090408	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2252102	C11orf17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8987000-9007200	Weak transcription	Brain Germinal Matrix	brain
2	chr11:8987000-9007200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr11:8987000-9010200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:8987000-9011000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:8987600-9005000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr11:8987600-9006400	Weak transcription	Colon Smooth Muscle	Colon
7	chr11:8987600-9010000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr11:8987600-9010000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr11:8987800-8999000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr11:8987800-9005000	Weak transcription	Brain Angular Gyrus	brain
11	chr11:8987800-9010200	Weak transcription	NHDF-Ad	bronchial
12	chr11:8987800-9012000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr11:8989200-8999000	Weak transcription	Fetal Intestine Small	intestine
14	chr11:8989600-9001400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr11:8989600-9002400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr11:8989600-9003400	Weak transcription	Fetal Stomach	stomach
17	chr11:8989600-9010000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:8989600-9011200	Weak transcription	Brain Anterior Caudate	brain
19	chr11:8989600-9019600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:8991800-9015600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr11:8992400-8999200	Weak transcription	Placenta	Placenta
22	chr11:8994000-9008600	Weak transcription	K562	blood
23	chr11:8996400-9005800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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