Variant report

Variant	rs4802085
Chromosome Location	chr19:41221513-41221514
allele	C/G
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	MAX	chr19:41221411-41221873	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	JUND	chr19:41220722-41223493	A549	lung:	n/a	chr19:41221814-41221824 chr19:41222178-41222189 chr19:41222080-41222091 chr19:41222081-41222091 chr19:41221813-41221825 chr19:41222081-41222091 chr19:41222917-41222926 chr19:41222081-41222091 chr19:41221815-41221823 chr19:41222179-41222189 chr19:41222081-41222091 chr19:41222081-41222090
4	POLR2A	chr19:41221379-41221771	GM12878	blood:	n/a	n/a
5	FOSL2	chr19:41221341-41222432	MCF-7	breast:	n/a	chr19:41221814-41221824 chr19:41222178-41222189 chr19:41222081-41222091 chr19:41221813-41221825 chr19:41222081-41222091 chr19:41222081-41222091 chr19:41221815-41221823 chr19:41222179-41222189 chr19:41222081-41222091 chr19:41222081-41222090
6	POLR2A	chr19:41220704-41223405	Raji	blood:	n/a	n/a
7	NR3C1	chr19:41221448-41221767	ECC-1	luminal epithelium:	n/a	chr19:41221588-41221597 chr19:41221693-41221702 chr19:41221664-41221682 chr19:41221584-41221597
8	SP1	chr19:41220495-41223600	A549	lung:	n/a	chr19:41222709-41222723 chr19:41220745-41220759 chr19:41222798-41222807 chr19:41222861-41222870 chr19:41221025-41221034 chr19:41222705-41222716 chr19:41222861-41222870 chr19:41222860-41222870 chr19:41221456-41221470 chr19:41222599-41222611 chr19:41222860-41222869 chr19:41222859-41222871 chr19:41221602-41221611 chr19:41222599-41222611 chr19:41222796-41222808 chr19:41221879-41221893 chr19:41222859-41222871 chr19:41222919-41222928 chr19:41221600-41221612 chr19:41222969-41222979 chr19:41222600-41222609 chr19:41222969-41222979
9	BCL3	chr19:41220248-41225401	A549	lung:	n/a	chr19:41225228-41225237 chr19:41222875-41222884 chr19:41222082-41222091 chr19:41222234-41222243
10	TEAD4	chr19:41221397-41221939	ECC-1	luminal epithelium:	n/a	n/a
11	RAD21	chr19:41221425-41221867	SK-N-SH_RA	brain:	n/a	chr19:41221630-41221642
12	JUND	chr19:41221491-41223085	K562	blood:	n/a	chr19:41221814-41221824 chr19:41222178-41222189 chr19:41222080-41222091 chr19:41222081-41222091 chr19:41221813-41221825 chr19:41222081-41222091 chr19:41222917-41222926 chr19:41222081-41222091 chr19:41221815-41221823 chr19:41222179-41222189 chr19:41222081-41222091 chr19:41222081-41222090
13	SIN3AK20	chr19:41221509-41221856	PFSK-1	brain:	n/a	n/a
14	NR3C1	chr19:41221279-41222407	A549	lung:	n/a	chr19:41221814-41221823 chr19:41221815-41221824 chr19:41221588-41221597 chr19:41221693-41221702 chr19:41221664-41221682 chr19:41221584-41221597
15	GATA3	chr19:41221383-41223122	MCF-7	breast:	n/a	chr19:41222790-41222798
16	IRF3	chr19:41220953-41221969	Hela-S3	cervix:	n/a	chr19:41221598-41221612
17	TCF12	chr19:41220427-41223301	SK-N-SH	brain:	n/a	chr19:41221137-41221145
18	RUNX3	chr19:41221350-41223167	GM12878	blood:	n/a	n/a
19	ZNF217	chr19:41221424-41221840	MCF-7	breast:	n/a	n/a
20	MAFK	chr19:41221370-41222810	IMR90	lung:	n/a	chr19:41221687-41221702 chr19:41222180-41222190 chr19:41221692-41221701 chr19:41221692-41221702 chr19:41221456-41221471 chr19:41221691-41221705 chr19:41221690-41221706
21	ZNF263	chr19:41221275-41223163	HEK293-T-REx	kidney:	n/a	chr19:41221462-41221471
22	SP1	chr19:41220643-41223291	HCT-116	colon:	n/a	chr19:41222709-41222723 chr19:41220745-41220759 chr19:41222798-41222807 chr19:41222861-41222870 chr19:41221025-41221034 chr19:41222705-41222716 chr19:41222861-41222870 chr19:41222860-41222870 chr19:41221456-41221470 chr19:41222599-41222611 chr19:41222860-41222869 chr19:41222859-41222871 chr19:41221602-41221611 chr19:41222599-41222611 chr19:41222796-41222808 chr19:41221879-41221893 chr19:41222859-41222871 chr19:41222919-41222928 chr19:41221600-41221612 chr19:41222969-41222979 chr19:41222600-41222609 chr19:41222969-41222979
23	MAX	chr19:41221159-41222903	MCF-7	breast:	n/a	chr19:41222713-41222723 chr19:41222082-41222091
24	POLR2A	chr19:41221313-41223239	Hela-S3	cervix:	n/a	n/a
25	STAT3	chr19:41221267-41222409	MCF10A-Er-Src	breast:	n/a	chr19:41222081-41222090 chr19:41221661-41221669 chr19:41222150-41222162 chr19:41221879-41221891 chr19:41221659-41221670
26	POLR2A	chr19:41220671-41221831	ECC-1	luminal epithelium:	n/a	n/a
27	CHD2	chr19:41220733-41221996	GM12878	blood:	n/a	chr19:41220935-41220945
28	POLR2A	chr19:41220316-41225389	H1-hESC	embryonic stem cell:	n/a	n/a
29	TBP	chr19:41221130-41223029	GM12878	blood:	n/a	n/a
30	USF1	chr19:41221396-41222288	A549	lung:	n/a	n/a
31	POLR2A	chr19:41221386-41221918	HUVEC	blood vessel:	n/a	n/a
32	TBP	chr19:41221357-41221875	HepG2	liver:	n/a	n/a
33	BHLHE40	chr19:41221184-41221879	K562	blood:	n/a	n/a
34	MAFK	chr19:41221473-41222321	K562	blood:	n/a	chr19:41221687-41221702 chr19:41222180-41222190 chr19:41221692-41221701 chr19:41221692-41221702 chr19:41221691-41221705 chr19:41221690-41221706
35	GATA3	chr19:41221335-41222975	MCF-7	breast:	n/a	chr19:41222790-41222798
36	ELF1	chr19:41220446-41221891	A549	lung:	n/a	chr19:41221003-41221016 chr19:41221005-41221014
37	JUND	chr19:41221436-41222946	MCF-7	breast:	n/a	chr19:41221814-41221824 chr19:41222178-41222189 chr19:41222080-41222091 chr19:41222081-41222091 chr19:41221813-41221825 chr19:41222081-41222091 chr19:41222917-41222926 chr19:41222081-41222091 chr19:41221815-41221823 chr19:41222179-41222189 chr19:41222081-41222091 chr19:41222081-41222090
38	CEBPB	chr19:41220757-41223142	A549	lung:	n/a	n/a
39	SIX5	chr19:41221000-41222979	A549	lung:	n/a	n/a
40	RELA	chr19:41220787-41221820	GM10847	blood:	n/a	n/a
41	ARID3A	chr19:41221063-41221814	HepG2	liver:	n/a	n/a
42	SIN3AK20	chr19:41220913-41223137	A549	lung:	n/a	n/a
43	POLR2A	chr19:41221274-41223569	GM12878	blood:	n/a	n/a
44	POLR2A	chr19:41221467-41223425	GM12878	blood:	n/a	n/a
45	CREB1	chr19:41221328-41221950	A549	lung:	n/a	n/a
46	TEAD4	chr19:41221309-41222508	SK-N-SH	brain:	n/a	n/a
47	GABPA	chr19:41221370-41223230	MCF-7	breast:	n/a	chr19:41221602-41221611
48	SMARCC1	chr19:41220859-41223014	Hela-S3	cervix:	n/a	chr19:41221815-41221824 chr19:41222081-41222090
49	NR3C1	chr19:41221362-41221756	ECC-1	luminal epithelium:	n/a	chr19:41221588-41221597 chr19:41221693-41221702 chr19:41221664-41221682 chr19:41221584-41221597
50	POLR2A	chr19:41221306-41223428	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41219466..41223288-chr19:41281896..41285456,5	MCF-7	breast:
2	chr19:41110008..41112738-chr19:41221401..41222982,2	MCF-7	breast:
3	chr19:41220672..41223321-chr19:41282772..41284711,3	K562	blood:
4	chr19:41221300..41223743-chr19:41303378..41306610,3	MCF-7	breast:
5	chr19:41220369..41226479-chr19:41305318..41310706,7	K562	blood:
6	chr19:41220938..41225137-chr19:41311275..41314518,5	K562	blood:
7	chr19:40949347..40951622-chr19:41220868..41223140,2	MCF-7	breast:
8	chr19:41221165..41222932-chr19:41261508..41263224,2	MCF-7	breast:
9	chr19:41220005..41225073-chr19:41230462..41235365,8	K562	blood:
10	chr19:41220377..41222544-chr19:41768201..41769798,2	MCF-7	breast:
11	chr19:41193561..41199772-chr19:41221208..41225709,11	K562	blood:
12	chr19:41213611..41215968-chr19:41219093..41222083,3	MCF-7	breast:
13	chr19:41207302..41211180-chr19:41220761..41224340,7	K562	blood:
14	chr19:41221472..41222399-chr7:92219229..92219756,2	Hela-S3	cervix:
15	chr19:41219701..41226727-chr19:41253156..41258804,17	K562	blood:
16	chr19:41219692..41221966-chr19:41769353..41771568,2	MCF-7	breast:
17	chr19:41205738..41209357-chr19:41220858..41225801,5	MCF-7	breast:
18	chr19:41188510..41190194-chr19:41220428..41221993,2	K562	blood:
19	chr19:41220807..41223667-chr19:41282098..41285361,4	MCF-7	breast:
20	chr19:41191453..41200740-chr19:41219595..41226457,20	MCF-7	breast:
21	chr19:40949565..40951989-chr19:41219354..41222014,2	K562	blood:
22	chr16:30669667..30670243-chr19:41221082..41221648,2	Hela-S3	cervix:
23	chr19:41187452..41189406-chr19:41221376..41223661,2	MCF-7	breast:
24	chr19:41220057..41225402-chr19:41302090..41307926,9	MCF-7	breast:
25	chr19:41220988..41222886-chr19:41267608..41270115,2	MCF-7	breast:
26	chr19:41221453..41223468-chr19:41246365..41247883,2	MCF-7	breast:
27	chr19:41220238..41223312-chr19:41303618..41307521,4	K562	blood:
28	chr19:41221436..41223725-chr19:41310201..41314445,5	MCF-7	breast:
29	chr19:41219701..41225554-chr19:41255271..41259667,13	K562	blood:
30	chr19:40948713..40950768-chr19:41219384..41222098,2	K562	blood:
31	chr19:41219625..41226874-chr19:41252287..41258959,29	MCF-7	breast:
32	chr19:41220720..41224635-chr19:41312175..41316788,5	MCF-7	breast:
33	chr19:41193720..41198590-chr19:41218677..41224410,19	MCF-7	breast:
34	chr19:41219350..41226574-chr19:41253922..41258567,22	MCF-7	breast:
35	chr19:41220581..41222873-chr19:41307320..41309933,2	MCF-7	breast:
36	chr19:41221142..41224353-chr19:41311383..41314668,3	K562	blood:

Variant related genes	Relation type
ITPKC	TF binding region
ADCK4	TF binding region
ENSG00000156860	Chromatin interaction
ENSG00000090006	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000167565	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000223284	Chromatin interaction
ENSG00000268797	Chromatin interaction
ENSG00000105323	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000268366	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000234545	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10425765	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11083566	0.96[CEU][hapmap];0.91[JPT][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11548478	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12976551	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1469427	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1870086	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1870087	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs2115239	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2246095	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2288451	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2290692	0.96[CEU][hapmap];0.91[JPT][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2290693	0.96[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2561535	0.88[ASN][1000 genomes]
rs2604882	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2604885	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2604887	0.90[ASN][1000 genomes]
rs2604913	0.81[CEU][hapmap]
rs3745216	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs3865452	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4802086	0.83[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs4802087	0.81[AMR][1000 genomes]
rs4803358	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6508944	0.87[ASN][1000 genomes]
rs7248468	0.96[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7248570	0.96[CEU][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7251246	0.96[CEU][hapmap];0.91[JPT][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7257602	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]
rs7260405	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8111960	0.96[CEU][hapmap];0.81[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4802085	ADCK4	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41219800-41222600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:41219800-41222800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr19:41220000-41222600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr19:41220200-41221600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr19:41220200-41221600	Flanking Active TSS	HSMMtube	muscle
6	chr19:41220200-41221600	Flanking Active TSS	NH-A	brain
7	chr19:41220200-41221800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:41220200-41221800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:41220200-41221800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:41220200-41221800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr19:41220200-41222000	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr19:41220200-41222600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr19:41220200-41222600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr19:41220200-41222600	Flanking Active TSS	Fetal Muscle Trunk	muscle
15	chr19:41220200-41222600	Flanking Active TSS	Fetal Muscle Leg	muscle
16	chr19:41220200-41222600	Flanking Active TSS	Dnd41	blood
17	chr19:41220200-41222600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr19:41220200-41222800	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr19:41220400-41221600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr19:41220400-41221600	Flanking Active TSS	Pancreas	Pancrea
21	chr19:41220400-41221600	Flanking Active TSS	Stomach Mucosa	stomach
22	chr19:41220400-41222000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:41220400-41222400	Flanking Active TSS	K562	blood
24	chr19:41220400-41222600	Flanking Active TSS	Primary B cells from peripheral blood	blood
25	chr19:41220400-41222600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
26	chr19:41220400-41222600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr19:41220400-41222600	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr19:41220400-41222600	Flanking Active TSS	Liver	Liver
29	chr19:41220400-41222600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr19:41220400-41222600	Flanking Active TSS	HUVEC	blood vessel
31	chr19:41220400-41222800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
32	chr19:41220400-41222800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr19:41220400-41225400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr19:41220400-41225600	Active TSS	H9 Cell Line	embryonic stem cell
35	chr19:41220400-41225800	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr19:41220400-41226800	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr19:41220600-41222000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr19:41220600-41224800	Active TSS	Right Ventricle	heart
39	chr19:41220600-41225200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr19:41220600-41225400	Active TSS	Left Ventricle	heart
41	chr19:41220600-41225400	Active TSS	Psoas Muscle	Psoas
42	chr19:41220600-41225600	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr19:41220600-41225600	Active TSS	Aorta	Aorta
44	chr19:41220600-41225800	Active TSS	Gastric	stomach
45	chr19:41220600-41226400	Active TSS	Right Atrium	heart
46	chr19:41220600-41227000	Active TSS	Esophagus	oesophagus
47	chr19:41220800-41221600	Active TSS	Brain Cingulate Gyrus	brain
48	chr19:41220800-41221800	Active TSS	Colonic Mucosa	Colon
49	chr19:41220800-41226200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr19:41221000-41221600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links