Variant report

Variant	rs10840228
Chromosome Location	chr11:9408426-9408427
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:9403958..9411793-chr11:9477944..9485616,22	K562	blood:
2	chr11:9406437..9409790-chr11:9593475..9595985,3	K562	blood:
3	chr11:9284656..9288251-chr11:9406150..9408599,6	K562	blood:
4	chr11:9334169..9339249-chr11:9404487..9409469,24	K562	blood:
5	chr11:9328102..9338305-chr11:9404480..9412498,38	K562	blood:
6	chr11:9328690..9334073-chr11:9404480..9408917,7	K562	blood:
7	chr11:9405101..9410331-chr11:9478772..9485340,14	K562	blood:

Variant related genes	Relation type
ENSG00000166483	Chromatin interaction
ENSG00000254884	Chromatin interaction
ENSG00000166478	Chromatin interaction
ENSG00000166471	Chromatin interaction
ENSG00000184014	Chromatin interaction
ENSG00000268403	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1020621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1020622	0.90[ASN][1000 genomes]
rs10437665	0.81[JPT][hapmap]
rs10743107	0.99[ASN][1000 genomes]
rs10770026	0.89[AMR][1000 genomes]
rs10770027	0.83[MEX][hapmap]
rs10770028	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]
rs10770029	0.99[ASN][1000 genomes]
rs10770032	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.99[ASN][1000 genomes]
rs10770033	0.90[ASN][1000 genomes]
rs10840229	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10840234	1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs10840235	1.00[ASW][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10840236	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10840237	0.83[AMR][1000 genomes];0.91[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	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11042329	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs11042343	0.83[MEX][hapmap]
rs11042348	0.93[ASN][1000 genomes]
rs11042349	0.87[ASN][1000 genomes]
rs11042350	0.90[ASN][1000 genomes]
rs11042353	0.90[ASN][1000 genomes]
rs11042355	0.90[ASN][1000 genomes]
rs11042356	0.90[ASN][1000 genomes]
rs11042366	0.94[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11042395	0.95[JPT][hapmap]
rs11826606	0.84[ASN][1000 genomes]
rs12225755	0.94[ASN][1000 genomes]
rs12271897	0.90[ASN][1000 genomes]
rs12282176	0.90[ASN][1000 genomes]
rs12296039	0.86[ASN][1000 genomes]
rs12418581	0.83[MEX][hapmap]
rs12790938	0.85[AMR][1000 genomes]
rs12795344	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12797567	0.93[ASN][1000 genomes]
rs12799672	0.86[ASN][1000 genomes]
rs12800802	0.90[ASN][1000 genomes]
rs2278900	0.95[JPT][hapmap]
rs2290423	0.87[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2290424	0.95[JPT][hapmap]
rs2290425	0.95[JPT][hapmap]
rs35781320	0.87[ASN][1000 genomes]
rs41369549	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4625466	0.83[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs4810	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4910048	0.81[JPT][hapmap]
rs4910051	0.83[MEX][hapmap]
rs4910053	0.95[JPT][hapmap]
rs6486306	0.96[ASN][1000 genomes]
rs6486307	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[ASN][1000 genomes]
rs6486359	0.90[ASN][1000 genomes]
rs6486361	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6486394	0.95[JPT][hapmap]
rs67548305	0.90[ASN][1000 genomes]
rs68060819	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7103931	0.80[ASN][1000 genomes]
rs7104568	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7114824	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7115477	0.83[GIH][hapmap];0.95[MEX][hapmap]
rs7122252	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7128033	0.88[AMR][1000 genomes]
rs723297	0.95[JPT][hapmap]
rs727405	0.95[JPT][hapmap]
rs729313	0.95[JPT][hapmap]
rs7395411	0.87[ASN][1000 genomes]
rs7396544	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7480643	0.85[GIH][hapmap];0.95[MEX][hapmap]
rs7926589	0.95[JPT][hapmap]
rs7927350	0.94[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs7944435	0.81[ASN][1000 genomes]
rs7944578	0.94[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7949973	0.90[ASN][1000 genomes]
rs8785	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9667574	0.82[ASN][1000 genomes]
rs972594	0.95[JPT][hapmap]
rs9787851	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv508617	chr11:9314027-9408562	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10840228	TEAD1	cis	cerebellum	SCAN
rs10840228	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	chr11:9405800-9408600	Active TSS	K562	blood
2	chr11:9405800-9409000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr11:9405800-9409000	Active TSS	Psoas Muscle	Psoas
4	chr11:9405800-9409200	Active TSS	Right Ventricle	heart
5	chr11:9406000-9408600	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr11:9406600-9408600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr11:9406600-9408800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr11:9406600-9409200	Transcr. at gene 5' and 3'	Dnd41	blood
9	chr11:9406800-9409000	Transcr. at gene 5' and 3'	A549	lung
10	chr11:9407000-9408800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:9407000-9409200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr11:9407200-9408600	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr11:9407200-9408800	Flanking Active TSS	HUVEC	blood vessel
14	chr11:9407200-9409000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
15	chr11:9407200-9409000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr11:9407200-9409800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:9407200-9410200	Weak transcription	Lung	lung
18	chr11:9407200-9425400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr11:9407200-9427000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:9407200-9430400	Weak transcription	Spleen	Spleen
21	chr11:9407200-9430600	Weak transcription	Esophagus	oesophagus
22	chr11:9407200-9430600	Weak transcription	Pancreas	Pancrea
23	chr11:9407200-9430800	Weak transcription	Gastric	stomach
24	chr11:9407400-9408600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:9407400-9408600	Enhancers	Colon Smooth Muscle	Colon
26	chr11:9407400-9408800	Enhancers	Brain Substantia Nigra	brain
27	chr11:9407400-9409000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr11:9407400-9409000	Enhancers	Primary hematopoietic stem cells	blood
29	chr11:9407400-9409000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr11:9407400-9409200	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr11:9407400-9409200	Enhancers	Brain Hippocampus Middle	brain
32	chr11:9407400-9409800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr11:9407400-9409800	Weak transcription	Fetal Stomach	stomach
34	chr11:9407400-9410000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr11:9407400-9410400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr11:9407400-9410600	Weak transcription	Ovary	ovary
37	chr11:9407400-9414200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr11:9407400-9414200	Weak transcription	Thymus	Thymus
39	chr11:9407400-9427000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr11:9407400-9427000	Weak transcription	Left Ventricle	heart
41	chr11:9407600-9408800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr11:9407600-9408800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr11:9407600-9408800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr11:9407600-9409000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
45	chr11:9407600-9409000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
46	chr11:9407600-9409000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr11:9407600-9409000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr11:9407600-9409000	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr11:9407600-9409000	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr11:9407600-9409200	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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