Variant report

Variant	rs10840262
Chromosome Location	chr11:9589840-9589841
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:9555259..9558705-chr11:9585485..9589925,6	MCF-7	breast:
2	chr11:9589366..9592285-chr11:9609804..9612652,2	MCF-7	breast:
3	chr11:9482098..9486375-chr11:9587030..9591762,7	K562	blood:
4	chr11:9405249..9407250-chr11:9587699..9590338,2	K562	blood:
5	chr11:9383299..9385895-chr11:9587946..9590537,2	MCF-7	breast:
6	chr11:9587790..9592116-chr11:9635065..9637852,3	MCF-7	breast:
7	chr11:9548940..9552769-chr11:9586407..9589954,6	MCF-7	breast:
8	chr11:9480903..9485608-chr11:9587733..9592274,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166478	Chromatin interaction
ENSG00000268403	Chromatin interaction
ENSG00000205339	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs4910479	0.81[ASN][1000 genomes]
rs7937639	0.86[CHB][hapmap]
rs7939541	0.81[JPT][hapmap];0.80[TSI][hapmap];0.80[ASN][1000 genomes]
rs921678	0.88[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427882	chr11:9431600-9626580	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv553467	chr11:9518551-9648721	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10840262	OR52B2	cis	cerebellum	SCAN
rs10840262	MICAL2	cis	parietal	SCAN
rs10840262	DKK3	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9579000-9590200	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr11:9583000-9590200	Weak transcription	Primary T cells from cord blood	blood
3	chr11:9584200-9594400	Enhancers	Stomach Mucosa	stomach
4	chr11:9584200-9594400	Weak transcription	Spleen	Spleen
5	chr11:9585200-9590800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr11:9585200-9593600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:9585200-9594400	Weak transcription	Esophagus	oesophagus
8	chr11:9585200-9594400	Weak transcription	Lung	lung
9	chr11:9586000-9591600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr11:9586200-9590400	Enhancers	Fetal Lung	lung
11	chr11:9586200-9590600	Enhancers	Hela-S3	cervix
12	chr11:9586200-9590600	Enhancers	NHLF	lung
13	chr11:9586400-9590000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr11:9586400-9594200	Enhancers	Fetal Intestine Small	intestine
15	chr11:9586600-9590000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr11:9586600-9590200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr11:9586600-9590200	Enhancers	NHDF-Ad	bronchial
18	chr11:9586600-9590800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr11:9586600-9590800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr11:9586600-9591800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr11:9586600-9594000	Enhancers	Placenta	Placenta
22	chr11:9586600-9594200	Enhancers	Fetal Intestine Large	intestine
23	chr11:9586800-9590800	Weak transcription	Right Atrium	heart
24	chr11:9586800-9591000	Weak transcription	Right Ventricle	heart
25	chr11:9587000-9590800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr11:9587800-9590200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr11:9588000-9590200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr11:9588000-9590800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr11:9588000-9590800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:9588000-9590800	Weak transcription	Left Ventricle	heart
31	chr11:9588000-9591000	Genic enhancers	Duodenum Smooth Muscle	Duodenum
32	chr11:9588000-9594400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr11:9588000-9594400	Weak transcription	Gastric	stomach
34	chr11:9588200-9590000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr11:9588200-9590000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr11:9588200-9590200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr11:9588200-9590400	Weak transcription	Fetal Muscle Leg	muscle
38	chr11:9588200-9590600	Weak transcription	Aorta	Aorta
39	chr11:9588200-9590600	Weak transcription	Small Intestine	intestine
40	chr11:9588200-9591200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr11:9588400-9590000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr11:9588400-9590200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr11:9588400-9590800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr11:9588600-9590200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr11:9588600-9590200	Enhancers	A549	lung
46	chr11:9588600-9590400	Weak transcription	GM12878-XiMat	blood
47	chr11:9588600-9590600	Enhancers	K562	blood
48	chr11:9588600-9590600	Enhancers	NH-A	brain
49	chr11:9588600-9591200	Weak transcription	Psoas Muscle	Psoas
50	chr11:9588600-9593800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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