Variant report

Variant	rs11042343
Chromosome Location	chr11:9441408-9441409
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9405090..9407610-chr11:9440133..9443604,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205339	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10770026	0.95[ASN][1000 genomes]
rs10770027	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs10840227	0.82[ASN][1000 genomes]
rs10840228	0.83[MEX][hapmap]
rs10840229	0.95[ASN][1000 genomes]
rs10840230	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10840233	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10840235	0.83[AMR][1000 genomes]
rs10840245	0.81[ASW][hapmap]
rs11042330	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11042338	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11042348	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11042349	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11608024	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12225755	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12418581	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12790938	0.94[ASN][1000 genomes]
rs12795344	0.81[AMR][1000 genomes]
rs12797567	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12800802	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12801513	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12801924	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12804650	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34177710	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41369549	0.82[GIH][hapmap]
rs4810	0.81[ASW][hapmap];0.82[GIH][hapmap]
rs4910051	0.91[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4910465	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7104568	0.82[GIH][hapmap]
rs7115477	0.85[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7128033	0.95[ASN][1000 genomes]
rs7480253	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7480643	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv427882	chr11:9431600-9626580	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv976476	chr11:9433496-9441932	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv442218	chr11:9435220-9441409	Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11042343	TEAD1	cis	cerebellum	SCAN
rs11042343	EIF4G2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9407600-9442000	Weak transcription	Fetal Brain Male	brain
2	chr11:9407600-9464000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:9416000-9456000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:9419200-9446600	Weak transcription	Small Intestine	intestine
5	chr11:9419600-9471000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:9419800-9444200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr11:9420600-9442000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr11:9420600-9450400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr11:9421000-9471200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:9423000-9470400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr11:9424200-9470400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr11:9424800-9468600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr11:9424800-9469000	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr11:9424800-9470600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:9425000-9468200	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr11:9425000-9468400	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr11:9425200-9467200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr11:9425600-9446800	Weak transcription	Colonic Mucosa	Colon
19	chr11:9425800-9468000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr11:9426200-9471600	Strong transcription	Dnd41	blood
21	chr11:9426400-9443000	Strong transcription	Hela-S3	cervix
22	chr11:9426800-9468400	Strong transcription	Primary B cells from peripheral blood	blood
23	chr11:9426800-9470600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr11:9427200-9466800	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr11:9427600-9471000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr11:9429800-9443000	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr11:9429800-9469000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr11:9430200-9459600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr11:9430200-9470200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:9430400-9457400	Strong transcription	A549	lung
31	chr11:9430400-9468200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr11:9431000-9453000	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr11:9431200-9443600	Weak transcription	Gastric	stomach
34	chr11:9431600-9449200	Weak transcription	Fetal Heart	heart
35	chr11:9431800-9468800	Weak transcription	Stomach Mucosa	stomach
36	chr11:9432800-9441800	Weak transcription	Brain Hippocampus Middle	brain
37	chr11:9432800-9450400	Weak transcription	Spleen	Spleen
38	chr11:9433000-9441600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr11:9433000-9441600	Weak transcription	Right Ventricle	heart
40	chr11:9433000-9442200	Weak transcription	NHLF	lung
41	chr11:9433000-9446800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr11:9433000-9449600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr11:9433000-9464000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr11:9433200-9441600	Weak transcription	Psoas Muscle	Psoas
45	chr11:9433200-9442000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr11:9433200-9442600	Weak transcription	Lung	lung
47	chr11:9433200-9443400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:9433200-9443400	Weak transcription	Pancreas	Pancrea
49	chr11:9433200-9444000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr11:9433200-9448600	Weak transcription	Brain Angular Gyrus	brain

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