Variant report

Variant	rs1029554
Chromosome Location	chr7:19747624-19747625
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr7:19747541-19747718	GM12878	blood:	n/a	n/a
2	MAX	chr7:19747457-19747835	K562	blood:	n/a	n/a
3	MXI1	chr7:19747451-19749751	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr7:19747521-19749005	MCF10A-Er-Src	breast:	n/a	n/a
5	E2F4	chr7:19747524-19747635	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

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:

No data

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

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10255236	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10266162	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10435066	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10435067	0.84[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs10486360	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs10486362	0.84[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs11974000	0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11976116	0.93[YRI][hapmap]
rs12673842	0.98[ASN][1000 genomes]
rs17141813	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs17141851	0.90[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2072184	1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs2072185	0.92[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2072186	0.85[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072187	1.00[CHB][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs2158381	0.93[ASN][1000 genomes]
rs2285925	0.83[ASW][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.81[ASN][1000 genomes]
rs2285927	0.86[JPT][hapmap];0.93[YRI][hapmap]
rs2285928	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28545597	0.87[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]
rs3948699	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]
rs4721820	1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs4721821	0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs58559474	0.94[ASN][1000 genomes]
rs6961959	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs72591432	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7802120	0.92[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7808579	0.86[YRI][hapmap]

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
rs1029554	TRA2A	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:19734800-19748000	Weak transcription	Lung	lung
2	chr7:19735800-19747800	Weak transcription	Colonic Mucosa	Colon
3	chr7:19736000-19748000	Weak transcription	Gastric	stomach
4	chr7:19738200-19748000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:19740000-19748000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:19742200-19747800	Weak transcription	Placenta	Placenta
7	chr7:19743600-19748000	Weak transcription	Esophagus	oesophagus
8	chr7:19745800-19747800	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr7:19745800-19748000	Flanking Active TSS	Dnd41	blood
10	chr7:19746000-19748200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:19746000-19748400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr7:19746400-19748000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr7:19746400-19748200	Flanking Active TSS	HUVEC	blood vessel
14	chr7:19746400-19748800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr7:19746400-19748800	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr7:19746400-19749200	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr7:19746600-19747800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr7:19746600-19747800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr7:19746600-19748000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr7:19746600-19748000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr7:19746600-19748800	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr7:19746600-19749000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr7:19746800-19747800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr7:19746800-19747800	Enhancers	Brain Substantia Nigra	brain
25	chr7:19746800-19748000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr7:19746800-19748000	Flanking Active TSS	NH-A	brain
27	chr7:19746800-19748400	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr7:19747000-19747800	Enhancers	Primary B cells from peripheral blood	blood
29	chr7:19747000-19747800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr7:19747000-19748000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr7:19747000-19748000	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr7:19747000-19748000	Enhancers	Pancreas	Pancrea
33	chr7:19747000-19748000	Enhancers	Small Intestine	intestine
34	chr7:19747000-19748800	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr7:19747000-19749000	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr7:19747000-19749000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr7:19747000-19749000	Active TSS	NHLF	lung
38	chr7:19747200-19747800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr7:19747200-19747800	Flanking Active TSS	Fetal Heart	heart
40	chr7:19747200-19747800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr7:19747200-19748000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr7:19747200-19748000	Weak transcription	Left Ventricle	heart
43	chr7:19747200-19748200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr7:19747200-19748400	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr7:19747200-19748800	Active TSS	H1 Cell Line	embryonic stem cell
46	chr7:19747200-19748800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr7:19747200-19748800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr7:19747200-19748800	Active TSS	K562	blood
49	chr7:19747200-19749000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr7:19747200-19749000	Active TSS	Fetal Kidney	kidney

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