Variant report

Variant	rs1136966
Chromosome Location	chr11:9042331-9042332
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	chr11:9041862..9044730-chr11:9157486..9160225,2	MCF-7	breast:
2	chr11:9037545..9039567-chr11:9040874..9042397,2	K562	blood:

Variant related genes	Relation type
ENSG00000175356	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10734639	0.81[MEX][hapmap]
rs10769974	0.82[MEX][hapmap]
rs10840151	0.82[MEX][hapmap]
rs10840170	1.00[CHB][hapmap]
rs10840186	1.00[CHB][hapmap]
rs10840188	1.00[CHB][hapmap]
rs11042196	1.00[CHB][hapmap]
rs11042197	1.00[CHB][hapmap]
rs11042215	1.00[CHB][hapmap]
rs11042217	1.00[CHB][hapmap]
rs1133833	0.85[MEX][hapmap];0.82[TSI][hapmap]
rs11607384	1.00[CHB][hapmap]
rs12794962	0.95[MEX][hapmap]
rs12796375	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1960181	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1969627	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984775	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984790	0.90[EUR][1000 genomes]
rs2016844	0.86[MEX][hapmap]
rs2056903	0.86[MEX][hapmap]
rs2060157	1.00[ASN][1000 genomes]
rs2116510	0.91[MEX][hapmap]
rs2133215	1.00[CHB][hapmap]
rs2163625	0.91[MEX][hapmap]
rs2173406	1.00[CHB][hapmap]
rs2568029	0.90[MEX][hapmap]
rs2568047	0.95[MEX][hapmap]
rs2568069	0.81[MEX][hapmap]
rs2653558	1.00[CHB][hapmap]
rs2653565	0.86[MEX][hapmap]
rs2653574	1.00[CHB][hapmap]
rs2653601	0.86[MEX][hapmap]
rs2653604	0.86[MEX][hapmap]
rs2653609	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742483	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742493	0.86[MEX][hapmap]
rs2742496	0.86[MEX][hapmap]
rs2742497	0.86[MEX][hapmap]
rs2742502	0.90[MEX][hapmap];0.85[TSI][hapmap]
rs2742514	0.82[MEX][hapmap]
rs2742519	0.82[MEX][hapmap]
rs34004082	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34191466	1.00[ASN][1000 genomes]
rs35578021	1.00[ASN][1000 genomes]
rs3751063	0.82[MEX][hapmap]
rs3751068	0.86[MEX][hapmap]
rs3763912	0.82[MEX][hapmap]
rs4061640	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4370967	0.91[MEX][hapmap]
rs4909951	0.81[MEX][hapmap]
rs4910068	0.90[MEX][hapmap];0.80[TSI][hapmap]
rs4910443	1.00[CHB][hapmap]
rs56277831	1.00[ASN][1000 genomes]
rs6486061	0.86[MEX][hapmap]
rs6486138	1.00[CHB][hapmap]
rs7108116	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7110170	0.84[EUR][1000 genomes]
rs7113467	1.00[CHB][hapmap]
rs7114013	1.00[CHB][hapmap]
rs7125458	0.95[MEX][hapmap];0.90[TSI][hapmap]
rs7129049	1.00[CHB][hapmap]
rs7130454	1.00[ASN][1000 genomes]
rs71476814	1.00[ASN][1000 genomes]
rs72856032	1.00[ASN][1000 genomes]
rs7396115	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7396130	1.00[CHB][hapmap]
rs7396541	1.00[CHB][hapmap]
rs7396840	1.00[CHB][hapmap]
rs7936201	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941341	1.00[CHB][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945759	1.00[CHB][hapmap]
rs7949022	1.00[CHB][hapmap]
rs7949349	1.00[CHB][hapmap]
rs9300096	0.82[MEX][hapmap]

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	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
2	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
3	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv896985	chr11:9013002-9152463	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1136966	RPL27A	cis	cerebellum	SCAN
rs1136966	NCF1C	trans	lymphoblastoid	seeQTL
rs1136966	C11orf17	cis	lymphoblastoid	seeQTL
rs1136966	C11orf17	cis	cerebellum	SCAN
rs1136966	HBD	cis	cerebellum	SCAN
rs1136966	C11orf17	Cis_1M	lymphoblastoid	RTeQTL
rs1136966	RPL27A	cis	parietal	SCAN
rs1136966	PRKCDBP	cis	parietal	SCAN
rs1136966	DENND5A	cis	lymphoblastoid	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9035200-9051800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:9036600-9048400	Weak transcription	Pancreas	Pancrea
3	chr11:9037600-9045000	Weak transcription	Fetal Brain Male	brain
4	chr11:9038200-9045200	Weak transcription	HSMMtube	muscle
5	chr11:9038200-9064000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr11:9038600-9047000	Weak transcription	Brain Substantia Nigra	brain
7	chr11:9038800-9047400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr11:9039000-9052000	Weak transcription	Spleen	Spleen
9	chr11:9039000-9058800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr11:9039600-9048200	Weak transcription	Fetal Stomach	stomach
11	chr11:9039600-9049600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr11:9039600-9052000	Weak transcription	Lung	lung
13	chr11:9039600-9057800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:9039800-9043200	Weak transcription	Fetal Muscle Leg	muscle
15	chr11:9039800-9043200	Weak transcription	Left Ventricle	heart
16	chr11:9039800-9044200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr11:9039800-9047200	Weak transcription	NHDF-Ad	bronchial
18	chr11:9040000-9044200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr11:9040000-9045400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr11:9040000-9047000	Weak transcription	Adipose Nuclei	Adipose
21	chr11:9041600-9042600	Enhancers	Stomach Smooth Muscle	stomach
22	chr11:9041800-9046000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr11:9041800-9052400	Weak transcription	Gastric	stomach
24	chr11:9042000-9044800	Enhancers	Fetal Lung	lung
25	chr11:9042200-9042400	Enhancers	Colonic Mucosa	Colon
26	chr11:9042200-9042600	Enhancers	Right Ventricle	heart
27	chr11:9042200-9042800	Enhancers	Right Atrium	heart
28	chr11:9042200-9048000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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