Variant report

Variant	rs2072185
Chromosome Location	chr7:19748700-19748701
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:652)
CpG islands
(count:183)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:652 , 50 per page) page: 1 2 3 4 5 6 7 ... 14

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL3	chr7:19748380-19749011	A549	lung:	n/a	chr7:19748739-19748748
2	MYC	chr7:19747937-19748976	K562	blood:	n/a	n/a
3	FOS	chr7:19748594-19748870	MCF10A-Er-Src	breast:	n/a	n/a
4	WRNIP1	chr7:19747963-19749467	GM12878	blood:	n/a	n/a
5	SMC3	chr7:19748580-19748980	GM12878	blood:	n/a	chr7:19748776-19748790 chr7:19748776-19748784
6	CTCF	chr7:19748700-19748850	AG10803	skin:	n/a	chr7:19748776-19748797 chr7:19748774-19748792 chr7:19748777-19748786
7	POLR2A	chr7:19748177-19749012	GM19099	blood:	n/a	n/a
8	TAF1	chr7:19748401-19748825	GM12891	blood:	n/a	n/a
9	POU2F2	chr7:19748382-19748894	GM12878	blood:	n/a	n/a
10	MYC	chr7:19748579-19748791	HUVEC	blood vessel:	n/a	n/a
11	YY1	chr7:19748406-19748900	HCT-116	colon:	n/a	chr7:19748631-19748643
12	SMC3	chr7:19748634-19748978	HepG2	liver:	n/a	chr7:19748776-19748790 chr7:19748776-19748784
13	BCL3	chr7:19748425-19748903	GM12878	blood:	n/a	chr7:19748739-19748748
14	POLR2A	chr7:19747828-19749044	Hela-S3	cervix:	n/a	n/a
15	ARID3A	chr7:19748325-19749082	K562	blood:	n/a	n/a
16	ELK1	chr7:19748517-19748949	Hela-S3	cervix:	n/a	n/a
17	STAT5A	chr7:19748456-19749007	K562	blood:	n/a	chr7:19748737-19748745
18	POU2F2	chr7:19748290-19748994	GM12878	blood:	n/a	n/a
19	FOXM1	chr7:19748316-19749075	GM12878	blood:	n/a	n/a
20	ELK1	chr7:19748410-19748773	K562	blood:	n/a	n/a
21	CREB1	chr7:19748077-19749095	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr7:19748243-19748913	A549	lung:	n/a	n/a
23	MYC	chr7:19748467-19748847	HepG2	liver:	n/a	n/a
24	TAF1	chr7:19748231-19748888	A549	lung:	n/a	n/a
25	USF2	chr7:19748548-19748881	GM12878	blood:	n/a	n/a
26	CTCF	chr7:19748408-19749116	HCT-116	colon:	n/a	chr7:19748776-19748797 chr7:19748774-19748792 chr7:19748777-19748786
27	CTCF	chr7:19748680-19748830	HPF	lung:	n/a	chr7:19748776-19748797 chr7:19748774-19748792 chr7:19748777-19748786
28	YY1	chr7:19748519-19748764	K562	blood:	n/a	chr7:19748631-19748643
29	CTCF	chr7:19748537-19748974	H1-hESC	embryonic stem cell:	n/a	chr7:19748776-19748797 chr7:19748774-19748792 chr7:19748777-19748786
30	USF2	chr7:19748568-19749319	Hela-S3	cervix:	n/a	n/a
31	CHD2	chr7:19748102-19748993	HepG2	liver:	n/a	n/a
32	PAX5	chr7:19748285-19748969	GM12878	blood:	n/a	n/a
33	CTCF	chr7:19748452-19748920	MCF-7	breast:	n/a	chr7:19748776-19748797 chr7:19748774-19748792 chr7:19748777-19748786
34	YY1	chr7:19748455-19748880	A549	lung:	n/a	chr7:19748631-19748643
35	MAX	chr7:19748461-19748978	HepG2	liver:	n/a	n/a
36	MXI1	chr7:19747814-19749025	GM12878	blood:	n/a	n/a
37	PAX5	chr7:19748500-19748915	GM12878	blood:	n/a	n/a
38	BRCA1	chr7:19748482-19748975	GM12878	blood:	n/a	n/a
39	RAD21	chr7:19748524-19748967	IMR90	lung:	n/a	chr7:19748775-19748794
40	CHD2	chr7:19748425-19748965	H1-hESC	embryonic stem cell:	n/a	n/a
41	ZNF143	chr7:19748445-19748957	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr7:19748068-19749273	NB4	blood:	n/a	n/a
43	STAT3	chr7:19748617-19748818	MCF10A-Er-Src	breast:	n/a	chr7:19748737-19748745
44	FOXP2	chr7:19748345-19748855	PFSK-1	brain:	n/a	n/a
45	TEAD4	chr7:19748362-19749026	ECC-1	luminal epithelium:	n/a	n/a
46	CHD1	chr7:19748216-19748954	GM12878	blood:	n/a	n/a
47	RAD21	chr7:19748672-19748875	GM12878	blood:	n/a	chr7:19748775-19748794
48	POLR2A	chr7:19748281-19748949	GM15510	blood:	n/a	n/a
49	MYC	chr7:19748206-19749065	A549	lung:	n/a	n/a
50	TAF1	chr7:19748409-19748854	SK-N-SH	brain:	n/a	n/a

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:19748670-19748720	H1-hESC	embryonic stem cell:	embryo
2	chr7:19748676-19748726	PANC-1	pancreas:	n/a
3	chr7:19748670-19748720	Caco-2	colon:	n/a
4	chr7:19748663-19748713	HEK293	kidney:	embryo
5	chr7:19748676-19748726	GM12891	blood:	n/a
6	chr7:19748663-19748713	SK-N-SH_RA	brain:	n/a
7	chr7:19748676-19748726	AG04449	skin:	fetal
8	chr7:19748663-19748713	GM12892	blood:	n/a
9	chr7:19748676-19748726	NB4	blood:	n/a
10	chr7:19748663-19748713	NHDF-neo	bronchial:	n/a
11	chr7:19748663-19748713	HIPEpiC	eye:	n/a
12	chr7:19748676-19748726	NT2-D1	testis:	n/a
13	chr7:19748676-19748726	A549	lung:	n/a
14	chr7:19748676-19748726	PrEC	prostate:	n/a
15	chr7:19748663-19748713	ProgFib	skin:	n/a
16	chr7:19748676-19748726	Jurkat	blood:	n/a
17	chr7:19748670-19748720	GM12892	blood:	n/a
18	chr7:19748670-19748720	T-47D	breast:	n/a
19	chr7:19748670-19748720	NB4	blood:	n/a
20	chr7:19748676-19748726	ECC-1	luminal epithelium:	n/a
21	chr7:19748676-19748726	HRE	kidney:	n/a
22	chr7:19748676-19748726	NHDF-neo	bronchial:	n/a
23	chr7:19748663-19748713	RPTEC	kidney:	n/a
24	chr7:19748670-19748720	HL-60	blood:	n/a
25	chr7:19748670-19748720	AG10803	skin:	n/a
26	chr7:19748670-19748720	HCT-116	colon:	n/a
27	chr7:19748663-19748713	U87	brain:	n/a
28	chr7:19748663-19748713	GM06990	blood:	n/a
29	chr7:19748670-19748720	BE2_C	brain:	n/a
30	chr7:19748663-19748713	PANC-1	pancreas:	n/a
31	chr7:19748676-19748726	LNCaP	prostate:	n/a
32	chr7:19748670-19748720	SK-N-SH_RA	brain:	n/a
33	chr7:19748670-19748720	HRE	kidney:	n/a
34	chr7:19748663-19748713	AG04449	skin:	fetal
35	chr7:19748676-19748726	AG04450	lung:	fetal
36	chr7:19748663-19748713	PrEC	prostate:	n/a
37	chr7:19748663-19748713	GM12878	blood:	n/a
38	chr7:19748676-19748726	HPAEpiC	pulmonary alveolar:	n/a
39	chr7:19748663-19748713	K562	blood:	n/a
40	chr7:19748676-19748726	HUVEC	blood vessel:	n/a
41	chr7:19748670-19748720	GM06990	blood:	n/a
42	chr7:19748670-19748720	HPAEpiC	pulmonary alveolar:	n/a
43	chr7:19748670-19748720	BJ	skin:	n/a
44	chr7:19748676-19748726	HMEC	breast:	n/a
45	chr7:19748676-19748726	GM06990	blood:	n/a
46	chr7:19748663-19748713	HL-60	blood:	n/a
47	chr7:19748670-19748720	PANC-1	pancreas:	n/a
48	chr7:19748676-19748726	BE2_C	brain:	n/a
49	chr7:19748670-19748720	HCM	heart:	n/a
50	chr7:19748663-19748713	HCT-116	colon:	n/a

(count:8 , 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	chr7:19737218..19740997-chr7:19747742..19750274,4	K562	blood:
5	chr1:53018395..53019315-chr7:19748309..19748892,2	NB4	blood:
6	chr7:19748380..19750241-chr7:20367987..20371074,3	MCF-7	breast:
7	chr7:19743433..19745474-chr7:19746532..19749255,3	K562	blood:
8	chr7:19740790..19742645-chr7:19746038..19748708,3	MCF-7	breast:

No data

Variant related genes	Relation type
MIR3146	TF binding region
MIR3146	CpG island
ENSG00000134744	Chromatin interaction
ENSG00000105855	Chromatin interaction
ENSG00000105849	Chromatin interaction
ENSG00000265932	Chromatin interaction
ENSG00000271133	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10255236	0.95[CHB][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10266162	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs1029554	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]
rs10435066	0.90[JPT][hapmap];0.84[YRI][hapmap];0.90[ASN][1000 genomes]
rs10435067	0.84[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10486360	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10486362	0.86[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs11974000	0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11976116	1.00[YRI][hapmap]
rs12673842	0.97[ASN][1000 genomes]
rs17141813	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17141851	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2072184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072186	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	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2158381	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2285925	0.92[ASW][hapmap];0.87[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2285927	0.93[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2285928	0.90[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs28545597	0.89[ASN][1000 genomes]
rs28587039	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28756683	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3948699	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs4721820	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4721821	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58559474	0.98[ASN][1000 genomes]
rs6961959	0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.96[ASN][1000 genomes]
rs72591432	0.91[ASN][1000 genomes]
rs7802120	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7808579	0.93[YRI][hapmap]

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
rs2072185	TRA2A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:19746400-19748800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr7:19746400-19748800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr7:19746400-19749200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr7:19746600-19748800	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr7:19746600-19749000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr7:19747000-19748800	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr7:19747000-19749000	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr7:19747000-19749000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:19747000-19749000	Active TSS	NHLF	lung
10	chr7:19747200-19748800	Active TSS	H1 Cell Line	embryonic stem cell
11	chr7:19747200-19748800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:19747200-19748800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:19747200-19748800	Active TSS	K562	blood
14	chr7:19747200-19749000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr7:19747200-19749000	Active TSS	Fetal Kidney	kidney
16	chr7:19747200-19749000	Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr7:19747200-19749000	Active TSS	GM12878-XiMat	blood
18	chr7:19747200-19749200	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr7:19747400-19748800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr7:19747400-19748800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr7:19747400-19748800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr7:19747400-19748800	Active TSS	Muscle Satellite Cultured Cells	--
23	chr7:19747400-19748800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:19747400-19748800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr7:19747400-19748800	Active TSS	Stomach Mucosa	stomach
26	chr7:19747400-19748800	Active TSS	HSMMtube	muscle
27	chr7:19747400-19749000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:19747400-19749000	Active TSS	Right Ventricle	heart
29	chr7:19747400-19749000	Active TSS	NHDF-Ad	bronchial
30	chr7:19747400-19749200	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr7:19747400-19749200	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr7:19747400-19749400	Active TSS	Ovary	ovary
33	chr7:19747600-19748800	Active TSS	H9 Cell Line	embryonic stem cell
34	chr7:19747600-19748800	Active TSS	A549	lung
35	chr7:19747600-19748800	Active TSS	Hela-S3	cervix
36	chr7:19747600-19748800	Active TSS	HMEC	breast
37	chr7:19747600-19748800	Active TSS	NHEK	skin
38	chr7:19747600-19749000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:19747600-19749000	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr7:19747600-19749000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr7:19747600-19749000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr7:19747600-19749000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr7:19747600-19749200	Active TSS	Aorta	Aorta
44	chr7:19747600-19749600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr7:19747800-19748800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr7:19747800-19748800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr7:19747800-19748800	Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr7:19747800-19748800	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr7:19747800-19748800	Active TSS	Colon Smooth Muscle	Colon
50	chr7:19747800-19748800	Active TSS	Fetal Intestine Large	intestine

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