Variant report

Variant	rs8110284
Chromosome Location	chr19:38422517-38422518
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	ZBTB33	chr19:38422506-38423382	A549	lung:	n/a	n/a
2	POLR2A	chr19:38422384-38423482	GM12892	blood:	n/a	n/a
3	TBP	chr19:38422446-38423165	GM12878	blood:	n/a	n/a
4	STAT3	chr19:38422413-38422774	GM12878	blood:	n/a	n/a
5	ATF3	chr19:38422396-38424733	A549	lung:	n/a	n/a
6	POLR2A	chr19:38422517-38423334	A549	lung:	n/a	n/a
7	SP1	chr19:38422277-38425218	A549	lung:	n/a	n/a
8	JUND	chr19:38422420-38423404	A549	lung:	n/a	n/a
9	FOXA2	chr19:38422444-38424138	A549	lung:	n/a	n/a
10	RUNX3	chr19:38422442-38423364	GM12878	blood:	n/a	n/a
11	ELF1	chr19:38422418-38423669	A549	lung:	n/a	n/a
12	MBD4	chr19:38422365-38422890	HepG2	liver:	n/a	n/a
13	POLR2A	chr19:38422467-38423254	HepG2	liver:	n/a	n/a
14	MAX	chr19:38422503-38423390	NB4	blood:	n/a	chr19:38422964-38422975 chr19:38422965-38422975 chr19:38422965-38422974 chr19:38422963-38422976 chr19:38422964-38422973 chr19:38422963-38422976 chr19:38422964-38422975 chr19:38422965-38422975 chr19:38422964-38422975
15	POLR2A	chr19:38422509-38423395	ECC-1	luminal epithelium:	n/a	n/a
16	WRNIP1	chr19:38422420-38423637	GM12878	blood:	n/a	n/a
17	SIN3AK20	chr19:38422399-38423661	A549	lung:	n/a	n/a
18	MAX	chr19:38422415-38423507	HepG2	liver:	n/a	chr19:38422964-38422975 chr19:38422965-38422975 chr19:38422965-38422974 chr19:38422963-38422976 chr19:38422964-38422973 chr19:38422963-38422976 chr19:38422964-38422975 chr19:38422965-38422975 chr19:38422964-38422975
19	ATF3	chr19:38422421-38423693	A549	lung:	n/a	n/a
20	FOXA2	chr19:38422459-38423365	A549	lung:	n/a	n/a
21	EP300	chr19:38422275-38424688	A549	lung:	n/a	chr19:38424431-38424440 chr19:38423719-38423728
22	ETS1	chr19:38422407-38423417	A549	lung:	n/a	n/a
23	EP300	chr19:38422209-38425183	A549	lung:	n/a	chr19:38424431-38424440 chr19:38423719-38423728
24	MAX	chr19:38422319-38425292	A549	lung:	n/a	chr19:38422964-38422975 chr19:38422965-38422975 chr19:38422965-38422974 chr19:38422963-38422976 chr19:38422964-38422973 chr19:38422963-38422976 chr19:38423719-38423728 chr19:38424431-38424440 chr19:38422964-38422975 chr19:38422965-38422975 chr19:38422964-38422975
25	SIN3AK20	chr19:38422301-38423585	A549	lung:	n/a	n/a
26	USF1	chr19:38422469-38423354	A549	lung:	n/a	chr19:38422964-38422975
27	POLR2A	chr19:38422450-38423540	PANC-1	pancreas:	n/a	n/a
28	IKZF1	chr19:38422504-38423532	GM12878	blood:	n/a	n/a
29	SIX5	chr19:38422263-38425474	A549	lung:	n/a	n/a
30	POLR2A	chr19:38422462-38423478	HL-60	blood:	n/a	n/a
31	POLR2A	chr19:38422455-38423301	GM12892	blood:	n/a	n/a
32	FOSL2	chr19:38422174-38424966	A549	lung:	n/a	chr19:38423719-38423728 chr19:38424431-38424440 chr19:38423719-38423727 chr19:38423720-38423727 chr19:38424430-38424439
33	HA-E2F1	chr19:38422439-38423442	MCF-7	breast:	n/a	n/a
34	TCF12	chr19:38421072-38425291	A549	lung:	n/a	chr19:38421714-38421722
35	POLR2A	chr19:38422472-38423981	GM12878	blood:	n/a	n/a
36	RUNX3	chr19:38422481-38423754	GM12878	blood:	n/a	n/a
37	HEY1	chr19:38422461-38423372	HepG2	liver:	n/a	n/a
38	POLR2A	chr19:38422418-38423447	H1-hESC	embryonic stem cell:	n/a	n/a
39	BCLAF1	chr19:38422454-38423239	GM12878	blood:	n/a	n/a
40	MYC	chr19:38422469-38423262	NB4	blood:	n/a	chr19:38422964-38422975 chr19:38422965-38422975 chr19:38422965-38422974 chr19:38422963-38422976 chr19:38422964-38422973 chr19:38422963-38422976 chr19:38422964-38422975 chr19:38422965-38422975 chr19:38422964-38422975
41	MAX	chr19:38422489-38423479	HCT-116	colon:	n/a	chr19:38422964-38422975 chr19:38422965-38422975 chr19:38422965-38422974 chr19:38422963-38422976 chr19:38422964-38422973 chr19:38422963-38422976 chr19:38422964-38422975 chr19:38422965-38422975 chr19:38422964-38422975
42	POLR2A	chr19:38422477-38423472	HepG2	liver:	n/a	n/a
43	RAD21	chr19:38422423-38423457	A549	lung:	n/a	chr19:38422831-38422841
44	MAX	chr19:38422485-38423576	HCT-116	colon:	n/a	chr19:38422964-38422975 chr19:38422965-38422975 chr19:38422965-38422974 chr19:38422963-38422976 chr19:38422964-38422973 chr19:38422963-38422976 chr19:38422964-38422975 chr19:38422965-38422975 chr19:38422964-38422975
45	STAT5A	chr19:38422482-38423258	GM12878	blood:	n/a	n/a
46	TAF1	chr19:38422436-38424579	A549	lung:	n/a	n/a
47	REST	chr19:38422035-38423605	A549	lung:	n/a	n/a
48	MAX	chr19:38422379-38425278	A549	lung:	n/a	chr19:38422964-38422975 chr19:38422965-38422975 chr19:38422965-38422974 chr19:38422963-38422976 chr19:38422964-38422973 chr19:38422963-38422976 chr19:38423719-38423728 chr19:38424431-38424440 chr19:38422964-38422975 chr19:38422965-38422975 chr19:38422964-38422975
49	REST	chr19:38422398-38424636	A549	lung:	n/a	n/a
50	FOSL2	chr19:38422450-38424042	A549	lung:	n/a	chr19:38423719-38423728 chr19:38423719-38423727 chr19:38423720-38423727

No.	Distal block	Cell Line	Cell type
1	chr19:38395556..38401665-chr19:38419693..38425913,12	MCF-7	breast:
2	chr19:38393450..38400778-chr19:38419865..38427350,17	MCF-7	breast:
3	chr19:38420982..38422890-chr19:38471015..38472804,2	MCF-7	breast:

Variant related genes	Relation type
SIPA1L3	TF binding region
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10401637	0.83[EUR][1000 genomes]
rs10404567	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10415548	0.83[CEU][hapmap]
rs10420746	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1119229	0.87[CEU][hapmap]
rs1291	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs12974225	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs1643462	0.86[EUR][1000 genomes]
rs1643463	0.86[EUR][1000 genomes]
rs1643466	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1643467	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1643468	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1643469	0.88[EUR][1000 genomes]
rs1725477	0.86[EUR][1000 genomes]
rs1725478	0.86[EUR][1000 genomes]
rs1725480	0.86[EUR][1000 genomes]
rs1725481	1.00[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs1725482	1.00[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs1725483	0.86[EUR][1000 genomes]
rs1725485	0.86[EUR][1000 genomes]
rs1725487	0.86[EUR][1000 genomes]
rs1725488	0.84[EUR][1000 genomes]
rs1725494	0.87[EUR][1000 genomes]
rs1725499	0.83[CEU][hapmap]
rs2075281	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs241932	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs2544718	0.87[EUR][1000 genomes]
rs3095726	0.93[CEU][hapmap];0.82[CHB][hapmap]
rs35209753	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs353398	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs353399	0.90[EUR][1000 genomes]
rs353400	0.90[EUR][1000 genomes]
rs353402	0.90[EUR][1000 genomes]
rs353403	0.88[EUR][1000 genomes]
rs353404	0.90[EUR][1000 genomes]
rs353407	0.90[EUR][1000 genomes]
rs353410	0.83[CEU][hapmap]
rs353411	0.83[CEU][hapmap]
rs353414	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs353415	1.00[CEU][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs353416	0.90[EUR][1000 genomes]
rs353417	0.90[EUR][1000 genomes]
rs353419	0.90[EUR][1000 genomes]
rs353420	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs353421	0.90[EUR][1000 genomes]
rs353423	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs353424	0.90[EUR][1000 genomes]
rs353425	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs353426	0.88[EUR][1000 genomes]
rs353427	0.90[EUR][1000 genomes]
rs353428	0.86[EUR][1000 genomes]
rs353429	0.83[EUR][1000 genomes]
rs353430	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3786869	0.83[CEU][hapmap]
rs4239516	0.82[CEU][hapmap]
rs4802135	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes]
rs4803524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4803551	0.87[CEU][hapmap]
rs4803573	0.87[CEU][hapmap]
rs705491	0.87[CEU][hapmap]
rs705492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs705493	0.87[CEU][hapmap]
rs705494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs705495	0.87[CEU][hapmap]
rs705500	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7250409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7250571	0.83[EUR][1000 genomes]
rs7250868	0.83[EUR][1000 genomes]
rs7252010	0.82[EUR][1000 genomes]
rs7258597	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs752878	0.86[EUR][1000 genomes]
rs8101858	0.81[EUR][1000 genomes]
rs8102579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs8107341	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8112706	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs8113521	0.83[CEU][hapmap]
rs833895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs833896	0.85[EUR][1000 genomes]
rs833897	0.86[EUR][1000 genomes]
rs833898	0.86[EUR][1000 genomes]
rs833914	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs833926	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs856300	0.93[CEU][hapmap];0.81[CHB][hapmap]
rs856304	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs9304572	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1064401	chr19:38387797-38427984	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1061106	chr19:38400149-38448723	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv544001	chr19:38400149-38448723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv960761	chr19:38419928-38422738	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8110284	WDR87	cis	Thyroid	GTEx
rs8110284	ZFP30	cis	Esophagus Muscularis	GTEx
rs8110284	ZNF571	cis	multi-tissue	Pritchard

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38398600-38422600	Weak transcription	Aorta	Aorta
2	chr19:38398800-38433800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:38399200-38422600	Weak transcription	Fetal Lung	lung
4	chr19:38399200-38424600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:38399600-38424000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr19:38399600-38424200	Weak transcription	Right Atrium	heart
7	chr19:38399600-38441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr19:38399800-38422600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr19:38402000-38422600	Weak transcription	Fetal Brain Male	brain
10	chr19:38405200-38422600	Weak transcription	Right Ventricle	heart
11	chr19:38405600-38422800	Weak transcription	Colon Smooth Muscle	Colon
12	chr19:38406000-38422600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr19:38411600-38422600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr19:38411800-38422600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr19:38411800-38426200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr19:38412000-38422600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr19:38412000-38423800	Weak transcription	Lung	lung
18	chr19:38412200-38422600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr19:38412200-38422800	Weak transcription	Adipose Nuclei	Adipose
20	chr19:38412200-38423000	Weak transcription	Thymus	Thymus
21	chr19:38417600-38422600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr19:38417600-38422600	Weak transcription	Ovary	ovary
23	chr19:38418600-38422600	Enhancers	Primary hematopoietic stem cells	blood
24	chr19:38418800-38422600	Enhancers	H1 Cell Line	embryonic stem cell
25	chr19:38418800-38425600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:38419400-38424800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr19:38419600-38422600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr19:38419800-38422600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:38419800-38422800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr19:38419800-38422800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr19:38420200-38422600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr19:38420200-38422600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr19:38420200-38425000	Weak transcription	Small Intestine	intestine
34	chr19:38420400-38422600	Weak transcription	Spleen	Spleen
35	chr19:38420600-38422600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr19:38421000-38422600	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr19:38421000-38422600	Enhancers	Liver	Liver
38	chr19:38421000-38423200	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr19:38421200-38422600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr19:38421200-38422600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:38421200-38422600	Enhancers	Muscle Satellite Cultured Cells	--
42	chr19:38421200-38422600	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr19:38421200-38422600	Enhancers	HMEC	breast
44	chr19:38421200-38424400	Enhancers	Fetal Heart	heart
45	chr19:38421200-38425000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr19:38421400-38422600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr19:38421400-38422600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr19:38421400-38422600	Enhancers	Primary B cells from peripheral blood	blood
49	chr19:38421600-38422800	Weak transcription	Gastric	stomach
50	chr19:38421600-38424800	Enhancers	Fetal Thymus	thymus

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