Variant report

Variant	rs2072186
Chromosome Location	chr7:19748007-19748008
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr7:19747937-19748976	K562	blood:	n/a	n/a
2	WRNIP1	chr7:19747963-19749467	GM12878	blood:	n/a	n/a
3	POLR2A	chr7:19747828-19749044	Hela-S3	cervix:	n/a	n/a
4	MXI1	chr7:19747814-19749025	GM12878	blood:	n/a	n/a
5	RELA	chr7:19747987-19749010	GM18951	blood:	n/a	n/a
6	POLR2A	chr7:19747717-19748887	HUVEC	blood vessel:	n/a	n/a
7	ATF1	chr7:19747985-19749187	K562	blood:	n/a	n/a
8	SIN3A	chr7:19747848-19748980	H1-hESC	embryonic stem cell:	n/a	n/a
9	RELA	chr7:19747905-19749028	GM19099	blood:	n/a	n/a
10	MXI1	chr7:19747966-19749119	HepG2	liver:	n/a	n/a
11	MAX	chr7:19747910-19749448	NB4	blood:	n/a	n/a
12	MXI1	chr7:19747962-19749209	IMR90	lung:	n/a	n/a
13	POLR2A	chr7:19748007-19749064	GM12878	blood:	n/a	n/a
14	POLR2A	chr7:19747859-19749028	K562	blood:	n/a	n/a
15	MXI1	chr7:19747451-19749751	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr7:19747745-19749178	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr7:19747957-19749105	H1-hESC	embryonic stem cell:	n/a	n/a
18	MYC	chr7:19747991-19749246	NB4	blood:	n/a	n/a
19	JUN	chr7:19747743-19749212	K562	blood:	n/a	n/a
20	POLR2A	chr7:19747521-19749005	MCF10A-Er-Src	breast:	n/a	n/a
21	REST	chr7:19747801-19749363	H1-neurons	neurons:	n/a	chr7:19748311-19748329 chr7:19748143-19748156
22	CHD1	chr7:19747902-19748728	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr7:19747924-19748984	K562	blood:	n/a	n/a
24	RAD21	chr7:19747807-19749356	SK-N-SH	brain:	n/a	chr7:19748775-19748794
25	POLR2A	chr7:19747744-19749060	GM12891	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:1498311..1499123-chr7:19747847..19748457,2	MCF-7	breast:
2	chr7:19744052..19746655-chr7:19747190..19748728,2	MCF-7	breast:
3	chr7:19740820..19745529-chr7:19747045..19749777,5	MCF-7	breast:
4	chr7:19745274..19751651-chr7:20366071..20371531,8	MCF-7	breast:
5	chr7:19737218..19740997-chr7:19747742..19750274,4	K562	blood:
6	chr7:19745589..19748453-chr7:19756261..19758585,2	K562	blood:
7	chr7:19746667..19748260-chr7:20349219..20351649,2	K562	blood:
8	chr7:19745703..19748379-chr7:20271088..20273693,2	K562	blood:
9	chr7:19743433..19745474-chr7:19746532..19749255,3	K562	blood:
10	chr7:19740790..19742645-chr7:19746038..19748708,3	MCF-7	breast:
11	chr7:19747017..19748692-chr7:20457391..20459961,2	MCF-7	breast:
12	chr7:6745135..6746643-chr7:19746904..19748412,2	K562	blood:

No data

Variant related genes	Relation type
MIR3146	TF binding region
ENSG00000271133	Chromatin interaction
ENSG00000265932	Chromatin interaction
ENSG00000164877	Chromatin interaction
ENSG00000164631	Chromatin interaction
ENSG00000105849	Chromatin interaction
ENSG00000105855	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10255236	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10266162	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1029554	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]
rs10435066	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10435067	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs10486360	0.87[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs10486362	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs11974000	0.96[ASN][1000 genomes]
rs12673842	0.95[ASN][1000 genomes]
rs17141813	0.87[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs17141819	0.89[YRI][hapmap]
rs17141832	0.89[YRI][hapmap]
rs17141835	0.89[YRI][hapmap]
rs17141851	0.88[CHD][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs2072184	0.87[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs2072185	0.87[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.91[LWK][hapmap];0.84[MKK][hapmap];0.93[ASN][1000 genomes]
rs2072187	0.86[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs2158381	0.96[ASN][1000 genomes]
rs2285925	0.86[JPT][hapmap]
rs2285927	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2285928	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs28545597	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28587039	0.95[ASN][1000 genomes]
rs28756683	0.95[ASN][1000 genomes]
rs3948699	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]
rs4721820	0.91[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs4721821	0.81[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs58559474	0.92[ASN][1000 genomes]
rs6948318	0.89[YRI][hapmap]
rs6961959	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs72591432	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7802120	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][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	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
5	nsv830918	chr7:19747674-19914527	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2072186	TRA2A	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:19746000-19748200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr7:19746000-19748400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr7:19746400-19748200	Flanking Active TSS	HUVEC	blood vessel
4	chr7:19746400-19748800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:19746400-19748800	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr7:19746400-19749200	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr7:19746600-19748800	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr7:19746600-19749000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr7:19746800-19748400	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr7:19747000-19748800	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr7:19747000-19749000	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr7:19747000-19749000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr7:19747000-19749000	Active TSS	NHLF	lung
14	chr7:19747200-19748200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr7:19747200-19748400	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr7:19747200-19748800	Active TSS	H1 Cell Line	embryonic stem cell
17	chr7:19747200-19748800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr7:19747200-19748800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr7:19747200-19748800	Active TSS	K562	blood
20	chr7:19747200-19749000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:19747200-19749000	Active TSS	Fetal Kidney	kidney
22	chr7:19747200-19749000	Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr7:19747200-19749000	Active TSS	GM12878-XiMat	blood
24	chr7:19747200-19749200	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr7:19747400-19748200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr7:19747400-19748200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr7:19747400-19748200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr7:19747400-19748200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr7:19747400-19748400	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr7:19747400-19748800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr7:19747400-19748800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr7:19747400-19748800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr7:19747400-19748800	Active TSS	Muscle Satellite Cultured Cells	--
34	chr7:19747400-19748800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr7:19747400-19748800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr7:19747400-19748800	Active TSS	Stomach Mucosa	stomach
37	chr7:19747400-19748800	Active TSS	HSMMtube	muscle
38	chr7:19747400-19749000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr7:19747400-19749000	Active TSS	Right Ventricle	heart
40	chr7:19747400-19749000	Active TSS	NHDF-Ad	bronchial
41	chr7:19747400-19749200	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr7:19747400-19749200	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr7:19747400-19749400	Active TSS	Ovary	ovary
44	chr7:19747600-19748200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr7:19747600-19748200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr7:19747600-19748200	Flanking Active TSS	Liver	Liver
47	chr7:19747600-19748200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
48	chr7:19747600-19748200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr7:19747600-19748400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr7:19747600-19748400	Flanking Active TSS	Primary B cells from cord blood	blood

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