Variant report

Variant	rs7257602
Chromosome Location	chr19:41224898-41224899
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:212)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:212 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41224814-41225247	K562	blood:	n/a	n/a
2	MAX	chr19:41220113-41225416	A549	lung:	n/a	chr19:41225122-41225132 chr19:41222713-41222723 chr19:41222082-41222091
3	BRCA1	chr19:41224728-41225024	HepG2	liver:	n/a	n/a
4	HDAC2	chr19:41224681-41225178	MCF-7	breast:	n/a	chr19:41224842-41224851
5	BHLHE40	chr19:41224784-41225309	GM12878	blood:	n/a	n/a
6	STAT1	chr19:41224865-41225057	GM12878	blood:	n/a	n/a
7	CEBPB	chr19:41224351-41225105	Hela-S3	cervix:	n/a	n/a
8	BCL3	chr19:41220248-41225401	A549	lung:	n/a	chr19:41225228-41225237 chr19:41222875-41222884 chr19:41222082-41222091 chr19:41222234-41222243
9	YY1	chr19:41224788-41225311	GM12892	blood:	n/a	n/a
10	POLR2A	chr19:41224689-41225297	HepG2	liver:	n/a	n/a
11	FOXA2	chr19:41224620-41225015	HepG2	liver:	n/a	n/a
12	CCNT2	chr19:41224812-41225114	K562	blood:	n/a	n/a
13	POLR2A	chr19:41224831-41225216	A549	lung:	n/a	n/a
14	SIN3A	chr19:41224792-41225171	H1-hESC	embryonic stem cell:	n/a	n/a
15	BHLHE40	chr19:41224714-41225221	HepG2	liver:	n/a	n/a
16	POLR2A	chr19:41220316-41225389	H1-hESC	embryonic stem cell:	n/a	n/a
17	NR3C1	chr19:41224798-41225076	ECC-1	luminal epithelium:	n/a	chr19:41225030-41225037
18	USF1	chr19:41224788-41225219	HepG2	liver:	n/a	n/a
19	MYC	chr19:41224847-41225198	MCF-7	breast:	n/a	chr19:41225122-41225132
20	SIX5	chr19:41224092-41225211	A549	lung:	n/a	n/a
21	USF2	chr19:41224855-41225042	K562	blood:	n/a	n/a
22	EBF1	chr19:41224880-41225643	GM12878	blood:	n/a	chr19:41225188-41225199
23	ZBTB33	chr19:41224630-41225131	HCT-116	colon:	n/a	n/a
24	USF1	chr19:41224684-41225273	ECC-1	luminal epithelium:	n/a	n/a
25	FOXA1	chr19:41224646-41225100	HepG2	liver:	n/a	n/a
26	FOXA2	chr19:41224232-41225184	A549	lung:	n/a	n/a
27	MAX	chr19:41224676-41225390	HepG2	liver:	n/a	chr19:41225122-41225132
28	USF2	chr19:41224809-41225148	HepG2	liver:	n/a	n/a
29	POLR2A	chr19:41224781-41225241	GM12878	blood:	n/a	n/a
30	POLR2A	chr19:41224614-41225231	A549	lung:	n/a	n/a
31	FOXA2	chr19:41224484-41225255	A549	lung:	n/a	n/a
32	MYC	chr19:41224871-41225334	MCF10A-Er-Src	breast:	n/a	chr19:41225122-41225132
33	USF1	chr19:41224819-41225087	HepG2	liver:	n/a	n/a
34	E2F6	chr19:41224767-41225182	K562	blood:	n/a	chr19:41224924-41224936
35	ZNF217	chr19:41224660-41225055	MCF-7	breast:	n/a	n/a
36	ZBTB7A	chr19:41224801-41225123	HepG2	liver:	n/a	n/a
37	BHLHE40	chr19:41224811-41225152	K562	blood:	n/a	n/a
38	E2F6	chr19:41224348-41225436	A549	lung:	n/a	chr19:41224924-41224936
39	NR2F2	chr19:41224499-41225292	MCF-7	breast:	n/a	n/a
40	RCOR1	chr19:41224324-41225198	Hela-S3	cervix:	n/a	n/a
41	MYC	chr19:41224872-41225136	H1-hESC	embryonic stem cell:	n/a	chr19:41225122-41225132
42	YY1	chr19:41224819-41225239	K562	blood:	n/a	n/a
43	EBF1	chr19:41224779-41225444	GM12878	blood:	n/a	chr19:41225188-41225199
44	HNF4A	chr19:41224727-41225261	HepG2	liver:	n/a	chr19:41224801-41224813
45	MAZ	chr19:41224490-41225193	Hela-S3	cervix:	n/a	n/a
46	MYC	chr19:41224583-41225268	K562	blood:	n/a	chr19:41225122-41225132
47	MXI1	chr19:41224813-41225106	K562	blood:	n/a	n/a
48	POLR2A	chr19:41224528-41225314	GM12878	blood:	n/a	n/a
49	REST	chr19:41223166-41225339	A549	lung:	n/a	n/a
50	EP300	chr19:41224885-41224908	K562	blood:	n/a	n/a

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41224831..41226803-chr19:41249457..41251875,2	K562	blood:
2	chr19:41224824..41227088-chr19:41310622..41313092,2	MCF-7	breast:
3	chr19:41220369..41226479-chr19:41305318..41310706,7	K562	blood:
4	chr19:41220938..41225137-chr19:41311275..41314518,5	K562	blood:
5	chr19:41220005..41225073-chr19:41230462..41235365,8	K562	blood:
6	chr19:41224337..41226397-chr19:41306033..41307626,2	K562	blood:
7	chr19:41193561..41199772-chr19:41221208..41225709,11	K562	blood:
8	chr19:41224377..41227042-chr19:41281377..41283783,3	MCF-7	breast:
9	chr19:41224564..41226766-chr3:161088576..161090786,2	MCF-7	breast:
10	chr19:41224657..41226437-chr19:41266206..41269077,2	MCF-7	breast:
11	chr19:41194805..41199772-chr19:41221674..41225965,11	K562	blood:
12	chr19:41219701..41226727-chr19:41253156..41258804,17	K562	blood:
13	chr19:41205738..41209357-chr19:41220858..41225801,5	MCF-7	breast:
14	chr19:41224721..41227148-chr19:41302837..41304471,2	K562	blood:
15	chr19:41191453..41200740-chr19:41219595..41226457,20	MCF-7	breast:
16	chr19:41220057..41225402-chr19:41302090..41307926,9	MCF-7	breast:
17	chr19:40971240..40973961-chr19:41221836..41225167,3	MCF-7	breast:
18	chr19:14628666..14629338-chr19:41224844..41225838,2	Hela-S3	cervix:
19	chr19:41219701..41225554-chr19:41255271..41259667,13	K562	blood:
20	chr19:41223813..41226637-chr19:41310296..41313871,3	MCF-7	breast:
21	chr19:41219625..41226874-chr19:41252287..41258959,29	MCF-7	breast:
22	chr19:41219350..41226574-chr19:41253922..41258567,22	MCF-7	breast:
23	chr19:41223981..41226562-chr19:41304181..41307698,5	MCF-7	breast:
24	chr19:41224545..41226553-chr19:41238187..41240048,2	MCF-7	breast:

No data

Variant related genes	Relation type
ADCK4	TF binding region
ENSG00000188493	Chromatin interaction
ENSG00000090013	Chromatin interaction
ENSG00000268797	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000160460	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000132002	Chromatin interaction
ENSG00000077312	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10425765	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11083566	0.93[ASW][hapmap];0.92[CEU][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11548478	0.85[AMR][1000 genomes]
rs12976551	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1469427	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1870086	0.88[CEU][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs1870087	0.87[ASW][hapmap];0.92[CEU][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs2115239	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2246095	0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2288451	0.84[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2290692	0.96[CEU][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2290693	0.92[CEU][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2561535	0.84[ASN][1000 genomes]
rs2604882	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2604885	0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2604887	0.85[ASN][1000 genomes]
rs3745216	0.83[CHB][hapmap]
rs3865452	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4802085	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4802086	0.90[JPT][hapmap];0.85[AMR][1000 genomes]
rs4802087	0.85[AMR][1000 genomes]
rs4803358	0.90[ASN][1000 genomes]
rs6508944	0.83[ASN][1000 genomes]
rs7248468	0.92[CEU][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7248570	0.93[ASW][hapmap];0.92[CEU][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7251246	0.93[ASW][hapmap];0.92[CEU][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7260405	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8111960	0.92[CEU][hapmap]
rs890934	0.81[ASW][hapmap];0.82[LWK][hapmap];0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1067017	chr19:41185992-41231251	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7257602	LIN7B	cis	parietal	SCAN
rs7257602	ADCK4	cis	Nerve Tibial	GTEx
rs7257602	SYMPK	cis	cerebellum	SCAN
rs7257602	PSG6	cis	parietal	SCAN
rs7257602	KCNN4	cis	cerebellum	SCAN
rs7257602	BCAT2	cis	cerebellum	SCAN
rs7257602	IRF2BP1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41220400-41225400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr19:41220400-41225600	Active TSS	H9 Cell Line	embryonic stem cell
3	chr19:41220400-41225800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr19:41220400-41226800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr19:41220600-41225200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr19:41220600-41225400	Active TSS	Left Ventricle	heart
7	chr19:41220600-41225400	Active TSS	Psoas Muscle	Psoas
8	chr19:41220600-41225600	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr19:41220600-41225600	Active TSS	Aorta	Aorta
10	chr19:41220600-41225800	Active TSS	Gastric	stomach
11	chr19:41220600-41226400	Active TSS	Right Atrium	heart
12	chr19:41220600-41227000	Active TSS	Esophagus	oesophagus
13	chr19:41220800-41226200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:41221000-41225200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr19:41221400-41226200	Active TSS	HMEC	breast
16	chr19:41221600-41225200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr19:41221600-41225400	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr19:41221600-41225600	Active TSS	NHEK	skin
19	chr19:41221600-41226400	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr19:41221800-41225600	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr19:41221800-41225800	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr19:41222000-41225000	Active TSS	H1 Cell Line	embryonic stem cell
23	chr19:41222200-41225000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr19:41222200-41225000	Active TSS	Ovary	ovary
25	chr19:41222200-41225200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr19:41222200-41225600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr19:41222200-41225600	Active TSS	Small Intestine	intestine
28	chr19:41222200-41225800	Active TSS	Placenta Amnion	Placenta Amnion
29	chr19:41222200-41226000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr19:41222400-41225200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:41222400-41225400	Active TSS	Fetal Intestine Large	intestine
32	chr19:41222400-41225400	Active TSS	Sigmoid Colon	Sigmoid Colon
33	chr19:41222400-41225600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr19:41222400-41225600	Active TSS	Pancreas	Pancrea
35	chr19:41222400-41226800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr19:41222400-41227000	Active TSS	Lung	lung
37	chr19:41222600-41225000	Active TSS	HSMM	muscle
38	chr19:41222600-41225400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:41222600-41225400	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr19:41222600-41225400	Active TSS	Fetal Kidney	kidney
41	chr19:41222600-41225600	Active TSS	NHDF-Ad	bronchial
42	chr19:41222600-41225800	Active TSS	NHLF	lung
43	chr19:41222600-41226200	Active TSS	HSMMtube	muscle
44	chr19:41223200-41225200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr19:41223200-41225200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr19:41223200-41225600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr19:41223200-41225800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr19:41223400-41225000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr19:41223400-41225200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
50	chr19:41223400-41225200	Flanking Active TSS	Primary B cells from peripheral blood	blood

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