Variant report

Variant	rs965467
Chromosome Location	chr11:86776992-86776993
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	chr11:86775970..86778427-chr11:86780728..86783153,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166575	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10792903	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1378880	0.87[GIH][hapmap];0.81[TSI][hapmap]
rs186198	1.00[YRI][hapmap]
rs2124577	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2124579	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs2124581	0.82[MEX][hapmap]
rs2374996	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2445537	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2445538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2445543	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2445549	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2445552	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2445564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2445565	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2445570	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2445581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2445587	0.82[JPT][hapmap]
rs2451066	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2512327	0.82[MEX][hapmap]
rs2512335	0.83[EUR][1000 genomes]
rs2512347	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.80[ASN][1000 genomes]
rs2512352	0.82[MEX][hapmap]
rs2512353	0.82[MEX][hapmap]
rs2512361	0.81[JPT][hapmap]
rs2512364	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2512370	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2512371	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2512373	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2512379	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2512382	0.82[MEX][hapmap]
rs2512390	0.82[MEX][hapmap]
rs2512392	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2512478	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2512486	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2512488	0.82[MEX][hapmap]
rs2512493	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2512498	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2512502	0.83[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2513206	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2513207	0.82[MEX][hapmap]
rs2513208	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2513219	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2513220	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2513225	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2513232	0.83[GIH][hapmap];0.83[JPT][hapmap]
rs2513234	0.94[ASN][1000 genomes]
rs3740659	0.83[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes]
rs564932	1.00[ASW][hapmap];0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1037042	chr11:86586876-86978492	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv541119	chr11:86586876-86978492	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv898058	chr11:86754948-86889284	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv898059	chr11:86754948-86949369	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1043562	chr11:86755535-87547185	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv541120	chr11:86755535-87547185	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv1046288	chr11:86757573-87158571	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
10	esv1844274	chr11:86776992-86872908	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs965467	TMEM126A	cis	cerebellum	SCAN
rs965467	TMEM135	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86750800-86780600	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr11:86750800-86782000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr11:86750800-86787400	Weak transcription	A549	lung
4	chr11:86751000-86786800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:86751000-86787400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:86751200-86785600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr11:86751400-86786400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr11:86751600-86787000	Weak transcription	Aorta	Aorta
9	chr11:86755200-86779000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr11:86755400-86780200	Weak transcription	Adipose Nuclei	Adipose
11	chr11:86755400-86780400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr11:86756400-86782800	Weak transcription	Fetal Intestine Small	intestine
13	chr11:86758200-86778600	Weak transcription	K562	blood
14	chr11:86758200-86780000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr11:86758200-86780400	Weak transcription	Fetal Muscle Leg	muscle
16	chr11:86758200-86783200	Weak transcription	Primary T cells from cord blood	blood
17	chr11:86758200-86786400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr11:86758400-86778800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:86767400-86779000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr11:86767800-86782800	Weak transcription	Left Ventricle	heart
21	chr11:86769000-86786400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr11:86769200-86786400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr11:86769200-86786800	Weak transcription	Brain Anterior Caudate	brain
24	chr11:86769200-86791200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr11:86769200-86792400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr11:86769400-86778600	Weak transcription	Liver	Liver
27	chr11:86769600-86784800	Weak transcription	Ovary	ovary
28	chr11:86769600-86786600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr11:86770200-86784200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr11:86770400-86808200	Weak transcription	HUVEC	blood vessel
31	chr11:86771000-86786600	Weak transcription	Fetal Brain Male	brain
32	chr11:86771200-86786800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr11:86771400-86778800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr11:86771800-86786000	Weak transcription	Fetal Lung	lung
35	chr11:86773000-86778800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr11:86773000-86783000	Weak transcription	NHDF-Ad	bronchial
37	chr11:86773000-86790800	Weak transcription	NHLF	lung
38	chr11:86773000-86792000	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr11:86774200-86782800	Weak transcription	Fetal Stomach	stomach
40	chr11:86774600-86792400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr11:86774800-86786400	Weak transcription	Lung	lung
42	chr11:86774800-86786800	Weak transcription	Pancreas	Pancrea
43	chr11:86774800-86786800	Weak transcription	Right Ventricle	heart
44	chr11:86774800-86787600	Weak transcription	NHEK	skin
45	chr11:86774800-86806400	Weak transcription	Small Intestine	intestine
46	chr11:86775000-86778600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr11:86775000-86786600	Weak transcription	Colon Smooth Muscle	Colon
48	chr11:86775200-86780400	Weak transcription	HepG2	liver
49	chr11:86775600-86786400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr11:86775600-86791400	Weak transcription	HSMM	muscle

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