Variant report

Variant	rs2072184
Chromosome Location	chr7:19748883-19748884
allele	C/T
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	BCL3	chr7:19748380-19749011	A549	lung:	n/a	chr7:19748739-19748748
2	MYC	chr7:19747937-19748976	K562	blood:	n/a	n/a
3	WRNIP1	chr7:19747963-19749467	GM12878	blood:	n/a	n/a
4	SMC3	chr7:19748580-19748980	GM12878	blood:	n/a	chr7:19748776-19748790 chr7:19748776-19748784
5	POLR2A	chr7:19748177-19749012	GM19099	blood:	n/a	n/a
6	POU2F2	chr7:19748382-19748894	GM12878	blood:	n/a	n/a
7	YY1	chr7:19748406-19748900	HCT-116	colon:	n/a	chr7:19748631-19748643
8	SMC3	chr7:19748634-19748978	HepG2	liver:	n/a	chr7:19748776-19748790 chr7:19748776-19748784
9	BCL3	chr7:19748425-19748903	GM12878	blood:	n/a	chr7:19748739-19748748
10	POLR2A	chr7:19747828-19749044	Hela-S3	cervix:	n/a	n/a
11	ARID3A	chr7:19748325-19749082	K562	blood:	n/a	n/a
12	ELK1	chr7:19748517-19748949	Hela-S3	cervix:	n/a	n/a
13	STAT5A	chr7:19748456-19749007	K562	blood:	n/a	chr7:19748737-19748745
14	POU2F2	chr7:19748290-19748994	GM12878	blood:	n/a	n/a
15	FOXM1	chr7:19748316-19749075	GM12878	blood:	n/a	n/a
16	CREB1	chr7:19748077-19749095	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr7:19748243-19748913	A549	lung:	n/a	n/a
18	TAF1	chr7:19748231-19748888	A549	lung:	n/a	n/a
19	CTCF	chr7:19748408-19749116	HCT-116	colon:	n/a	chr7:19748776-19748797 chr7:19748774-19748792 chr7:19748777-19748786
20	CTCF	chr7:19748537-19748974	H1-hESC	embryonic stem cell:	n/a	chr7:19748776-19748797 chr7:19748774-19748792 chr7:19748777-19748786
21	USF2	chr7:19748568-19749319	Hela-S3	cervix:	n/a	n/a
22	CHD2	chr7:19748102-19748993	HepG2	liver:	n/a	n/a
23	PAX5	chr7:19748285-19748969	GM12878	blood:	n/a	n/a
24	CTCF	chr7:19748740-19748890	NHDF-neo	bronchial:	n/a	chr7:19748776-19748797 chr7:19748774-19748792 chr7:19748777-19748786
25	CTCF	chr7:19748452-19748920	MCF-7	breast:	n/a	chr7:19748776-19748797 chr7:19748774-19748792 chr7:19748777-19748786
26	MAX	chr7:19748461-19748978	HepG2	liver:	n/a	n/a
27	MXI1	chr7:19747814-19749025	GM12878	blood:	n/a	n/a
28	PAX5	chr7:19748500-19748915	GM12878	blood:	n/a	n/a
29	BRCA1	chr7:19748482-19748975	GM12878	blood:	n/a	n/a
30	RAD21	chr7:19748524-19748967	IMR90	lung:	n/a	chr7:19748775-19748794
31	CHD2	chr7:19748425-19748965	H1-hESC	embryonic stem cell:	n/a	n/a
32	ZNF143	chr7:19748445-19748957	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr7:19748068-19749273	NB4	blood:	n/a	n/a
34	TEAD4	chr7:19748362-19749026	ECC-1	luminal epithelium:	n/a	n/a
35	CTCF	chr7:19748740-19748890	HUVEC	blood vessel:	n/a	chr7:19748776-19748797 chr7:19748774-19748792 chr7:19748777-19748786
36	CHD1	chr7:19748216-19748954	GM12878	blood:	n/a	n/a
37	POLR2A	chr7:19748281-19748949	GM15510	blood:	n/a	n/a
38	MYC	chr7:19748206-19749065	A549	lung:	n/a	n/a
39	MAX	chr7:19748422-19749011	Hela-S3	cervix:	n/a	n/a
40	SP1	chr7:19748400-19748927	GM12878	blood:	n/a	chr7:19748727-19748736 chr7:19748727-19748737 chr7:19748727-19748737
41	CTCF	chr7:19748618-19749004	K562	blood:	n/a	chr7:19748776-19748797 chr7:19748774-19748792 chr7:19748777-19748786
42	CTCF	chr7:19748456-19748912	GM19239	blood:	n/a	chr7:19748776-19748797 chr7:19748774-19748792 chr7:19748777-19748786
43	CHD2	chr7:19748247-19749250	K562	blood:	n/a	n/a
44	MAX	chr7:19748253-19748982	Hela-S3	cervix:	n/a	n/a
45	RELA	chr7:19747987-19749010	GM18951	blood:	n/a	n/a
46	CTCF	chr7:19748591-19748914	Pancreas_OC	pancreas:	n/a	chr7:19748776-19748797 chr7:19748774-19748792 chr7:19748777-19748786
47	POU2F2	chr7:19748353-19748953	GM12891	blood:	n/a	n/a
48	MAX	chr7:19748455-19749026	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr7:19747717-19748887	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr7:19748204-19749031	PBDE	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:19748860-19748910	T-47D	breast:	n/a
2	chr7:19748860-19748910	NHDF-neo	bronchial:	n/a
3	chr7:19748860-19748910	H1-hESC	embryonic stem cell:	embryo
4	chr7:19748860-19748910	ovcar-3	ovarian:	n/a
5	chr7:19748860-19748910	AG04450	lung:	fetal
6	chr7:19748860-19748910	RPTEC	kidney:	n/a
7	chr7:19748860-19748910	LNCaP	prostate:	n/a
8	chr7:19748860-19748910	NB4	blood:	n/a
9	chr7:19748860-19748910	AG10803	skin:	n/a
10	chr7:19748860-19748910	MCF-7	breast:	n/a
11	chr7:19748860-19748910	ProgFib	skin:	n/a
12	chr7:19748860-19748910	K562	blood:	n/a
13	chr7:19748860-19748910	HUVEC	blood vessel:	n/a
14	chr7:19748860-19748910	AG04449	skin:	fetal
15	chr7:19748860-19748910	GM12892	blood:	n/a
16	chr7:19748860-19748910	HRCEpiC	kidney:	n/a
17	chr7:19748860-19748910	NT2-D1	testis:	n/a
18	chr7:19748860-19748910	HepG2	liver:	n/a
19	chr7:19748860-19748910	ECC-1	luminal epithelium:	n/a
20	chr7:19748860-19748910	AG09309	skin:	n/a
21	chr7:19748860-19748910	A549	lung:	n/a
22	chr7:19748860-19748910	PFSK-1	brain:	n/a
23	chr7:19748860-19748910	NHBE	bronchial:	n/a
24	chr7:19748860-19748910	HRE	kidney:	n/a
25	chr7:19748860-19748910	HEK293	kidney:	embryo
26	chr7:19748860-19748910	MCF10A-Er-Src	breast:	n/a
27	chr7:19748860-19748910	SKMC	muscle:	n/a
28	chr7:19748860-19748910	HCT-116	colon:	n/a
29	chr7:19748860-19748910	GM19239	blood:	n/a
30	chr7:19748860-19748910	AoSMC	blood vessel:	n/a
31	chr7:19748860-19748910	HCPEpiC	choroid plexus:	n/a
32	chr7:19748860-19748910	GM12891	blood:	n/a
33	chr7:19748860-19748910	GM06990	blood:	n/a
34	chr7:19748860-19748910	Hela-S3	cervix:	n/a
35	chr7:19748860-19748910	HNPCEpiC	eye:	n/a
36	chr7:19748860-19748910	SK-N-SH	brain:	n/a
37	chr7:19748860-19748910	NH-A	brain:	n/a
38	chr7:19748860-19748910	IMR90	lung:	fetal
39	chr7:19748860-19748910	SAEC	small airway:	n/a
40	chr7:19748860-19748910	HMEC	breast:	n/a
41	chr7:19748860-19748910	HCM	heart:	n/a
42	chr7:19748860-19748910	HIPEpiC	eye:	n/a
43	chr7:19748860-19748910	PrEC	prostate:	n/a
44	chr7:19748860-19748910	CMK	blood:	n/a
45	chr7:19748860-19748910	SK-N-MC	brain:	n/a
46	chr7:19748860-19748910	HEEpiC	esophagus:	n/a
47	chr7:19748860-19748910	Hepatocyte	liver:	n/a
48	chr7:19748860-19748910	HCF	heart:	n/a
49	chr7:19748860-19748910	BE2_C	brain:	n/a
50	chr7:19748860-19748910	AG09319	gingival:	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:19748857..19751346-chr7:20255213..20257656,2	K562	blood:
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:

Variant related genes	Relation type
TWISTNB	TF binding region
MIR3146	TF binding region
MIR3146	CpG island
TWISTNB	CpG island
ENSG00000265932	Chromatin interaction
ENSG00000105849	Chromatin interaction
ENSG00000105855	Chromatin interaction
ENSG00000233834	Chromatin interaction
ENSG00000183742	Chromatin interaction
ENSG00000134744	Chromatin interaction
ENSG00000271133	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10255236	0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs10266162	1.00[ASW][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs1029554	1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs10435066	0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs10435067	1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10486360	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10486362	0.84[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11974000	0.97[ASN][1000 genomes]
rs12673842	0.96[ASN][1000 genomes]
rs17141813	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17141851	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2072185	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];0.81[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs2072187	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2158381	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2189566	0.80[ASN][1000 genomes]
rs2285925	0.87[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2285927	0.93[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2285928	1.00[ASW][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs28402966	0.80[ASN][1000 genomes]
rs28545597	0.89[ASN][1000 genomes]
rs28587039	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28756683	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3948699	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs4721820	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4721821	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58559474	0.98[ASN][1000 genomes]
rs6961959	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs72591432	0.91[ASN][1000 genomes]
rs7802120	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.93[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2072184	TWISTNB	cis	parietal	SCAN
rs2072184	TRA2A	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:19746400-19749200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr7:19746600-19749000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr7:19747000-19749000	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr7:19747000-19749000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:19747000-19749000	Active TSS	NHLF	lung
6	chr7:19747200-19749000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr7:19747200-19749000	Active TSS	Fetal Kidney	kidney
8	chr7:19747200-19749000	Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr7:19747200-19749000	Active TSS	GM12878-XiMat	blood
10	chr7:19747200-19749200	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr7:19747400-19749000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:19747400-19749000	Active TSS	Right Ventricle	heart
13	chr7:19747400-19749000	Active TSS	NHDF-Ad	bronchial
14	chr7:19747400-19749200	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr7:19747400-19749200	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr7:19747400-19749400	Active TSS	Ovary	ovary
17	chr7:19747600-19749000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr7:19747600-19749000	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr7:19747600-19749000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr7:19747600-19749000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:19747600-19749000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr7:19747600-19749200	Active TSS	Aorta	Aorta
23	chr7:19747600-19749600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr7:19747800-19749000	Active TSS	Brain Angular Gyrus	brain
25	chr7:19747800-19749000	Active TSS	Brain Cingulate Gyrus	brain
26	chr7:19747800-19749000	Active TSS	Fetal Heart	heart
27	chr7:19747800-19749000	Active TSS	Fetal Muscle Leg	muscle
28	chr7:19747800-19749000	Active TSS	Fetal Stomach	stomach
29	chr7:19747800-19749000	Active TSS	Psoas Muscle	Psoas
30	chr7:19747800-19749000	Active TSS	Thymus	Thymus
31	chr7:19747800-19749200	Active TSS	Colonic Mucosa	Colon
32	chr7:19747800-19749200	Active TSS	Fetal Brain Female	brain
33	chr7:19747800-19749200	Active TSS	Fetal Muscle Trunk	muscle
34	chr7:19747800-19749400	Active TSS	Brain Germinal Matrix	brain
35	chr7:19748000-19749000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr7:19748000-19749000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr7:19748000-19749000	Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr7:19748000-19749000	Active TSS	Duodenum Mucosa	Duodenum
39	chr7:19748000-19749000	Active TSS	Left Ventricle	heart
40	chr7:19748000-19749000	Active TSS	NH-A	brain
41	chr7:19748000-19749200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr7:19748000-19749200	Active TSS	Brain Anterior Caudate	brain
43	chr7:19748000-19749200	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr7:19748000-19749200	Active TSS	Fetal Brain Male	brain
45	chr7:19748000-19749400	Active TSS	Stomach Smooth Muscle	stomach
46	chr7:19748200-19749000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr7:19748200-19749000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr7:19748200-19749000	Active TSS	Brain Hippocampus Middle	brain
49	chr7:19748200-19749200	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr7:19748200-19749200	Active TSS	Brain Substantia Nigra	brain

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