Variant report

Variant	rs10770028
Chromosome Location	chr11:9420412-9420413
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:9417229..9422139-chr11:9482004..9484870,5	K562	blood:
2	chr11:9334599..9337963-chr11:9419653..9422855,3	K562	blood:
3	chr11:9334599..9336423-chr11:9420019..9421528,2	K562	blood:
4	chr11:9418157..9420498-chr11:9423191..9424773,2	MCF-7	breast:
5	chr11:9387912..9390461-chr11:9419141..9421304,2	K562	blood:
6	chr11:9419108..9421359-chr11:9425279..9427169,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166471	Chromatin interaction
ENSG00000268403	Chromatin interaction
ENSG00000205339	Chromatin interaction
ENSG00000166478	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1020621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1020622	0.89[ASN][1000 genomes]
rs10437665	0.81[JPT][hapmap]
rs10743107	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10770026	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10770029	1.00[ASN][1000 genomes]
rs10770032	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10770033	0.89[ASN][1000 genomes]
rs10840228	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10840229	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10840234	1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs10840235	0.93[ASW][hapmap];0.91[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10840236	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10840237	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10840238	0.90[ASN][1000 genomes]
rs10840243	0.95[JPT][hapmap]
rs10840245	0.95[JPT][hapmap]
rs10840253	0.86[JPT][hapmap]
rs11042328	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11042329	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs11042330	0.82[AMR][1000 genomes]
rs11042348	0.92[ASN][1000 genomes]
rs11042349	0.87[ASN][1000 genomes]
rs11042350	0.84[GIH][hapmap];0.90[ASN][1000 genomes]
rs11042353	0.89[ASN][1000 genomes]
rs11042355	0.89[ASN][1000 genomes]
rs11042356	0.89[ASN][1000 genomes]
rs11042366	0.94[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs11042395	0.95[JPT][hapmap]
rs11826606	0.84[ASN][1000 genomes]
rs12225755	0.94[ASN][1000 genomes]
rs12271897	0.90[ASN][1000 genomes]
rs12282176	0.89[ASN][1000 genomes]
rs12296039	0.85[ASN][1000 genomes]
rs12790938	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12795344	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12797567	0.92[ASN][1000 genomes]
rs12799672	0.85[ASN][1000 genomes]
rs12800802	0.90[ASN][1000 genomes]
rs12801924	0.82[AMR][1000 genomes]
rs2278900	0.95[JPT][hapmap]
rs2290423	0.87[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2290424	0.95[JPT][hapmap]
rs2290425	0.95[JPT][hapmap]
rs35781320	0.86[ASN][1000 genomes]
rs41369549	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4625466	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs4810	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4910048	0.81[JPT][hapmap]
rs4910051	0.82[AMR][1000 genomes]
rs4910053	0.95[JPT][hapmap]
rs6486306	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6486307	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6486359	0.89[ASN][1000 genomes]
rs6486361	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6486394	0.95[JPT][hapmap]
rs67548305	0.89[ASN][1000 genomes]
rs68060819	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7104568	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7114824	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7115477	0.91[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7122252	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7128033	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs723297	0.95[JPT][hapmap]
rs727405	0.95[JPT][hapmap]
rs729313	0.95[JPT][hapmap]
rs7395411	0.87[ASN][1000 genomes]
rs7396544	0.89[ASN][1000 genomes]
rs7480643	0.82[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7926589	0.95[JPT][hapmap]
rs7927350	0.94[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs7944578	0.87[ASW][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs7949973	0.89[ASN][1000 genomes]
rs8785	1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9667574	0.81[ASN][1000 genomes]
rs972594	0.95[JPT][hapmap]
rs9787851	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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	nsv916534	chr11:9188436-9516241	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1055078	chr11:9252857-9538877	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10770028	TEAD1	cis	cerebellum	SCAN
rs10770028	IPO7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9407200-9425400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr11:9407200-9427000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:9407200-9430400	Weak transcription	Spleen	Spleen
4	chr11:9407200-9430600	Weak transcription	Esophagus	oesophagus
5	chr11:9407200-9430600	Weak transcription	Pancreas	Pancrea
6	chr11:9407200-9430800	Weak transcription	Gastric	stomach
7	chr11:9407400-9427000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr11:9407400-9427000	Weak transcription	Left Ventricle	heart
9	chr11:9407600-9431400	Weak transcription	HSMMtube	muscle
10	chr11:9407600-9442000	Weak transcription	Fetal Brain Male	brain
11	chr11:9407600-9464000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr11:9407800-9425400	Weak transcription	Fetal Muscle Leg	muscle
13	chr11:9407800-9427000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr11:9408000-9424800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr11:9408200-9431000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr11:9408400-9428400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr11:9408800-9426400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr11:9408800-9427000	Weak transcription	Fetal Brain Female	brain
19	chr11:9408800-9431200	Weak transcription	Brain Substantia Nigra	brain
20	chr11:9409000-9421000	Weak transcription	NHLF	lung
21	chr11:9409000-9422800	Weak transcription	HUVEC	blood vessel
22	chr11:9409000-9424800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr11:9409000-9424800	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr11:9409000-9427000	Weak transcription	Liver	Liver
25	chr11:9409000-9427200	Weak transcription	HMEC	breast
26	chr11:9409200-9425600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr11:9409200-9427000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr11:9409200-9427200	Weak transcription	Psoas Muscle	Psoas
29	chr11:9410400-9425600	Weak transcription	Lung	lung
30	chr11:9411200-9421200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr11:9411200-9424800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr11:9414000-9425800	Weak transcription	Fetal Intestine Large	intestine
33	chr11:9414400-9424800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr11:9414400-9425800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr11:9414800-9421200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr11:9414800-9425800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr11:9414800-9426200	Weak transcription	Thymus	Thymus
38	chr11:9415000-9421000	Weak transcription	HepG2	liver
39	chr11:9415400-9426000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr11:9415800-9422600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr11:9415800-9430000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr11:9416000-9423000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr11:9416000-9456000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:9416200-9424800	Weak transcription	Fetal Thymus	thymus
45	chr11:9416400-9421000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr11:9417200-9421200	Weak transcription	HSMM	muscle
47	chr11:9417800-9420600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr11:9418000-9420600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr11:9418000-9420600	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr11:9418000-9421600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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