Variant report

Variant	rs7904
Chromosome Location	chr7:5273121-5273122
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	chr7:5272109..5273708-chr7:5323100..5324631,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs28434488	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4072666	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4446650	0.87[ASN][1000 genomes]
rs4720529	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4720537	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4720539	0.82[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4724462	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62441950	0.87[ASN][1000 genomes]
rs6954461	0.84[ASN][1000 genomes]
rs6956071	0.89[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6956950	0.86[ASN][1000 genomes]

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	nsv530968	chr7:4572250-5418004	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
3	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
4	nsv916396	chr7:5128917-5370805	Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
6	nsv887390	chr7:5224407-5411296	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv887391	chr7:5224407-5572132	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	292 gene(s)	inside rSNPs	diseases
8	nsv830889	chr7:5248157-5427465	Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv8034	chr7:5257953-5417973	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
10	nsv887392	chr7:5263194-5359680	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7904	TEAD4	trans	lymphoblastoid	seeQTL
rs7904	SLC29A4	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5231400-5279800	Weak transcription	Fetal Brain Male	brain
2	chr7:5231800-5273400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:5234000-5274800	Weak transcription	Stomach Mucosa	stomach
4	chr7:5237400-5273400	Strong transcription	Dnd41	blood
5	chr7:5248400-5273200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr7:5249000-5273200	Strong transcription	Fetal Muscle Trunk	muscle
7	chr7:5249000-5273600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr7:5249000-5273600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr7:5249200-5273400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:5249200-5273400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr7:5249200-5273400	Strong transcription	Duodenum Smooth Muscle	Duodenum
12	chr7:5249200-5273400	Strong transcription	Fetal Stomach	stomach
13	chr7:5249200-5273400	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chr7:5249200-5273600	Strong transcription	Fetal Intestine Small	intestine
15	chr7:5249600-5273400	Strong transcription	Right Ventricle	heart
16	chr7:5249800-5273600	Strong transcription	Fetal Brain Female	brain
17	chr7:5254000-5273400	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr7:5254000-5273400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr7:5254200-5280000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr7:5254600-5273600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr7:5258000-5279600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr7:5261000-5273400	Strong transcription	Colon Smooth Muscle	Colon
23	chr7:5261800-5273400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr7:5262400-5273400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr7:5262400-5273400	Strong transcription	Gastric	stomach
26	chr7:5266600-5276200	Weak transcription	Fetal Kidney	kidney
27	chr7:5267400-5279800	Weak transcription	Right Atrium	heart
28	chr7:5268200-5273400	Strong transcription	Thymus	Thymus
29	chr7:5268200-5280000	Weak transcription	Psoas Muscle	Psoas
30	chr7:5269200-5273400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:5269400-5273400	Genic enhancers	Spleen	Spleen
32	chr7:5269800-5273200	Genic enhancers	Fetal Thymus	thymus
33	chr7:5269800-5274800	Weak transcription	K562	blood
34	chr7:5270200-5273400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr7:5270200-5277000	Weak transcription	HSMMtube	muscle
36	chr7:5270200-5279800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr7:5270600-5273400	Strong transcription	Esophagus	oesophagus
38	chr7:5271000-5276800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr7:5271000-5276800	Weak transcription	NHDF-Ad	bronchial
40	chr7:5271000-5279800	Weak transcription	A549	lung
41	chr7:5271000-5279800	Weak transcription	HMEC	breast
42	chr7:5271200-5274600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr7:5271200-5277800	Weak transcription	HepG2	liver
44	chr7:5271200-5279600	Weak transcription	NH-A	brain
45	chr7:5271200-5280000	Weak transcription	Colonic Mucosa	Colon
46	chr7:5271400-5279600	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr7:5271400-5279800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr7:5271400-5280000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr7:5271600-5273400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr7:5271600-5280000	Weak transcription	HUVEC	blood vessel

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