Variant report

Variant	rs4082668
Chromosome Location	chr11:8822601-8822602
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8715578..8718169-chr11:8819916..8823970,3	MCF-7	breast:
2	chr11:8709766..8713200-chr11:8820077..8823864,3	K562	blood:

Variant related genes	Relation type
ENSG00000166441	Chromatin interaction
ENSG00000166444	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10743086	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10743090	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769961	0.84[CEU][hapmap]
rs10840119	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10840120	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10840122	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10840124	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11042052	0.90[CEU][hapmap]
rs11042064	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11042073	0.84[EUR][1000 genomes]
rs11042074	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12269980	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12287694	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12289240	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12291552	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12420964	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16906037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2316863	0.83[CEU][hapmap]
rs3763917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3763919	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3913547	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4370937	0.88[CEU][hapmap]
rs4929918	0.83[CEU][hapmap]
rs55902154	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60869409	0.98[EUR][1000 genomes]
rs6484007	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6484606	0.89[CEU][hapmap]
rs7105372	0.94[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap]
rs7131166	0.88[CEU][hapmap]
rs72858278	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv553447	chr11:8792622-8825966	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv527920	chr11:8816695-8856822	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4082668	TMEM9B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8797800-8827200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:8800800-8825800	Weak transcription	Brain Angular Gyrus	brain
3	chr11:8800800-8827400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:8801600-8827400	Weak transcription	Esophagus	oesophagus
5	chr11:8809000-8830200	Weak transcription	Fetal Brain Male	brain
6	chr11:8809200-8826600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr11:8809200-8829200	Weak transcription	Fetal Kidney	kidney
8	chr11:8811800-8827000	Weak transcription	HMEC	breast
9	chr11:8811800-8828600	Weak transcription	Hela-S3	cervix
10	chr11:8811800-8828800	Weak transcription	Aorta	Aorta
11	chr11:8811800-8830400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr11:8811800-8830600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:8814200-8828400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr11:8814800-8825400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr11:8815000-8827800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:8815200-8826800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr11:8815600-8825200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr11:8815800-8827800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:8816400-8825400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:8816400-8831800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:8816600-8826600	Weak transcription	Brain Anterior Caudate	brain
22	chr11:8816600-8827400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr11:8816600-8828400	Weak transcription	NHDF-Ad	bronchial
24	chr11:8816600-8828800	Weak transcription	Brain Substantia Nigra	brain
25	chr11:8816600-8830000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr11:8816600-8830600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr11:8816800-8825200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr11:8816800-8828600	Weak transcription	Small Intestine	intestine
29	chr11:8817000-8828600	Weak transcription	Fetal Intestine Large	intestine
30	chr11:8817200-8825600	Weak transcription	Spleen	Spleen
31	chr11:8817200-8828600	Weak transcription	Fetal Intestine Small	intestine
32	chr11:8817400-8828200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr11:8817600-8825000	Weak transcription	NHLF	lung
34	chr11:8819000-8825600	Weak transcription	Adipose Nuclei	Adipose
35	chr11:8819200-8826600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:8819400-8825200	Strong transcription	Fetal Muscle Leg	muscle
37	chr11:8819800-8828600	Weak transcription	Osteobl	bone
38	chr11:8819800-8829800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr11:8820000-8823200	Enhancers	Pancreas	Pancrea
40	chr11:8820000-8826200	Strong transcription	HSMMtube	muscle
41	chr11:8820000-8828200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr11:8820200-8823400	Enhancers	Ovary	ovary
43	chr11:8820200-8823800	Weak transcription	NH-A	brain
44	chr11:8820400-8824200	Enhancers	Left Ventricle	heart
45	chr11:8820600-8823000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr11:8820600-8823000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:8820600-8823000	Enhancers	Right Atrium	heart
48	chr11:8820600-8823000	Genic enhancers	Stomach Smooth Muscle	stomach
49	chr11:8820600-8823200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:8820600-8826400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast

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