Variant report

Variant	rs3948699
Chromosome Location	chr7:19747283-19747284
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:19747115-19747315	HUVEC	blood vessel:	n/a	n/a
2	FOS	chr7:19746842-19747289	HUVEC	blood vessel:	n/a	chr7:19747062-19747069 chr7:19747060-19747070 chr7:19747061-19747069 chr7:19747061-19747069 chr7:19747060-19747070 chr7:19747060-19747070 chr7:19747060-19747070 chr7:19747059-19747070
3	POLR2A	chr7:19747001-19747545	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:19744052..19746655-chr7:19747190..19748728,2	MCF-7	breast:
2	chr7:19740820..19745529-chr7:19747045..19749777,5	MCF-7	breast:
3	chr7:19745274..19751651-chr7:20366071..20371531,8	MCF-7	breast:
4	chr7:19745589..19748453-chr7:19756261..19758585,2	K562	blood:
5	chr7:19746667..19748260-chr7:20349219..20351649,2	K562	blood:
6	chr7:19745703..19748379-chr7:20271088..20273693,2	K562	blood:
7	chr7:19743433..19745474-chr7:19746532..19749255,3	K562	blood:
8	chr7:19740790..19742645-chr7:19746038..19748708,3	MCF-7	breast:
9	chr7:19745703..19747865-chr7:20271912..20273693,2	K562	blood:
10	chr7:19747017..19748692-chr7:20457391..20459961,2	MCF-7	breast:
11	chr7:6745135..6746643-chr7:19746904..19748412,2	K562	blood:

Variant related genes	Relation type
MIR3146	TF binding region
ENSG00000271133	Chromatin interaction
ENSG00000105855	Chromatin interaction
ENSG00000265932	Chromatin interaction
ENSG00000164631	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10255236	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10266162	0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs1029554	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10435066	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10435067	0.82[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs10486360	0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs10486362	0.82[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs11974000	0.97[ASN][1000 genomes]
rs12673842	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs17141813	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs17141851	0.86[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2072184	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs2072185	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs2072186	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072187	0.95[CHB][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs2158381	0.93[ASN][1000 genomes]
rs2285925	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2285927	0.86[JPT][hapmap]
rs2285928	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs28545597	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28587039	0.92[ASN][1000 genomes]
rs28756683	0.92[ASN][1000 genomes]
rs4721820	0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs4721821	0.90[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs58559474	0.94[ASN][1000 genomes]
rs6961959	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs72591432	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7802120	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

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	nsv1018601	chr7:19272360-20008881	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1033223	chr7:19682192-20461375	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv538795	chr7:19682192-20461375	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv524807	chr7:19714156-19803925	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3948699	TRA2A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:19730400-19747400	Weak transcription	HSMMtube	muscle
2	chr7:19733000-19747400	Weak transcription	Spleen	Spleen
3	chr7:19733800-19747400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr7:19734400-19747400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr7:19734800-19748000	Weak transcription	Lung	lung
6	chr7:19735800-19747800	Weak transcription	Colonic Mucosa	Colon
7	chr7:19736000-19748000	Weak transcription	Gastric	stomach
8	chr7:19736200-19747600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr7:19738200-19748000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:19740000-19748000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr7:19741800-19747600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr7:19742200-19747800	Weak transcription	Placenta	Placenta
13	chr7:19743400-19747600	Weak transcription	Aorta	Aorta
14	chr7:19743600-19748000	Weak transcription	Esophagus	oesophagus
15	chr7:19744200-19747400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr7:19745400-19747400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr7:19745400-19747400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr7:19745600-19747400	Enhancers	Fetal Brain Male	brain
19	chr7:19745800-19747600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr7:19745800-19747600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr7:19745800-19747600	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr7:19745800-19747800	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr7:19745800-19748000	Flanking Active TSS	Dnd41	blood
24	chr7:19746000-19747400	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr7:19746000-19747400	Enhancers	Fetal Brain Female	brain
26	chr7:19746000-19747600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr7:19746000-19748200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr7:19746000-19748400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:19746400-19747400	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr7:19746400-19747400	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr7:19746400-19747400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr7:19746400-19747400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr7:19746400-19747400	Enhancers	Brain Germinal Matrix	brain
34	chr7:19746400-19747600	Enhancers	Liver	Liver
35	chr7:19746400-19748000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr7:19746400-19748200	Flanking Active TSS	HUVEC	blood vessel
37	chr7:19746400-19748800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr7:19746400-19748800	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr7:19746400-19749200	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr7:19746600-19747400	Enhancers	Adipose Nuclei	Adipose
41	chr7:19746600-19747400	Enhancers	Brain Hippocampus Middle	brain
42	chr7:19746600-19747400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr7:19746600-19747400	Enhancers	Fetal Lung	lung
44	chr7:19746600-19747400	Flanking Active TSS	HepG2	liver
45	chr7:19746600-19747400	Enhancers	HSMM	muscle
46	chr7:19746600-19747600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr7:19746600-19747600	Enhancers	Primary T cells fromperipheralblood	blood
48	chr7:19746600-19747600	Enhancers	Brain Anterior Caudate	brain
49	chr7:19746600-19747800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr7:19746600-19747800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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