Variant report

Variant	rs62112287
Chromosome Location	chr19:38422917-38422918
allele	A/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	ZBTB33	chr19:38422506-38423382	A549	lung:	n/a	n/a
2	ESR1	chr19:38422911-38423390	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr19:38422384-38423482	GM12892	blood:	n/a	n/a
4	TBP	chr19:38422446-38423165	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	RELA	chr19:38422564-38423321	GM19099	blood:	n/a	n/a
9	USF1	chr19:38422692-38423408	ECC-1	luminal epithelium:	n/a	chr19:38422964-38422975
10	ESR1	chr19:38422843-38423413	ECC-1	luminal epithelium:	n/a	n/a
11	CTBP2	chr19:38422892-38424066	H1-hESC	embryonic stem cell:	n/a	n/a
12	STAT3	chr19:38422845-38423143	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr19:38422809-38423132	MCF10A-Er-Src	breast:	n/a	n/a
14	JUND	chr19:38422420-38423404	A549	lung:	n/a	n/a
15	TEAD4	chr19:38422850-38423353	MCF-7	breast:	n/a	n/a
16	USF1	chr19:38422530-38423210	A549	lung:	n/a	chr19:38422964-38422975
17	TEAD4	chr19:38422734-38423397	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr19:38422820-38423272	GM12892	blood:	n/a	n/a
19	RAD21	chr19:38422571-38423219	HepG2	liver:	n/a	chr19:38422831-38422841
20	USF2	chr19:38422777-38423181	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr19:38422796-38423101	K562	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
22	POLR2A	chr19:38422573-38423386	HL-60	blood:	n/a	n/a
23	FOXA2	chr19:38422444-38424138	A549	lung:	n/a	n/a
24	POLR2A	chr19:38422536-38423169	HepG2	liver:	n/a	n/a
25	RUNX3	chr19:38422442-38423364	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:38422694-38423439	MCF-7	breast:	n/a	n/a
27	ELF1	chr19:38422418-38423669	A549	lung:	n/a	n/a
28	EP300	chr19:38422877-38423416	T-47D	breast:	n/a	n/a
29	POLR2A	chr19:38422627-38423345	HepG2	liver:	n/a	n/a
30	MAX	chr19:38422640-38423417	H1-hESC	embryonic stem cell:	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
31	TAF1	chr19:38422600-38423271	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr19:38422467-38423254	HepG2	liver:	n/a	n/a
33	MYC	chr19:38422803-38423274	MCF-7	breast:	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
34	MXI1	chr19:38422696-38423241	H1-hESC	embryonic stem cell:	n/a	chr19:38422964-38422973 chr19:38422966-38422975
35	POLR2A	chr19:38422594-38423280	GM12891	blood:	n/a	n/a
36	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
37	POLR2A	chr19:38422509-38423395	ECC-1	luminal epithelium:	n/a	n/a
38	WRNIP1	chr19:38422420-38423637	GM12878	blood:	n/a	n/a
39	SIN3AK20	chr19:38422399-38423661	A549	lung:	n/a	n/a
40	TEAD4	chr19:38422624-38423497	HepG2	liver:	n/a	n/a
41	NFIC	chr19:38422598-38423705	GM12878	blood:	n/a	n/a
42	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
43	FOS	chr19:38422599-38423179	MCF10A-Er-Src	breast:	n/a	n/a
44	MXI1	chr19:38422582-38423368	HepG2	liver:	n/a	chr19:38422964-38422973 chr19:38422966-38422975
45	NFIC	chr19:38422565-38423484	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr19:38422662-38423234	H1-hESC	embryonic stem cell:	n/a	n/a
47	ATF3	chr19:38422421-38423693	A549	lung:	n/a	n/a
48	FOXA2	chr19:38422459-38423365	A549	lung:	n/a	n/a
49	TEAD4	chr19:38422889-38423466	HCT-116	colon:	n/a	n/a
50	EP300	chr19:38422275-38424688	A549	lung:	n/a	chr19:38424431-38424440 chr19:38423719-38423728

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

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

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs62110229	0.81[ASN][1000 genomes]
rs62110230	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62110232	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62112272	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62112273	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112274	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62112275	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112277	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62112280	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112282	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112288	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112289	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112291	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62120128	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62120129	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62120130	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62120131	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7257838	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7258680	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8105754	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38398800-38433800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr19:38399200-38424600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:38399600-38424000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr19:38399600-38424200	Weak transcription	Right Atrium	heart
5	chr19:38399600-38441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr19:38411800-38426200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr19:38412000-38423800	Weak transcription	Lung	lung
8	chr19:38412200-38423000	Weak transcription	Thymus	Thymus
9	chr19:38418800-38425600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr19:38419400-38424800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:38420200-38425000	Weak transcription	Small Intestine	intestine
12	chr19:38421000-38423200	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr19:38421200-38424400	Enhancers	Fetal Heart	heart
14	chr19:38421200-38425000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:38421600-38424800	Enhancers	Fetal Thymus	thymus
16	chr19:38421800-38423800	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr19:38421800-38425400	Enhancers	Fetal Muscle Trunk	muscle
18	chr19:38421800-38425400	Enhancers	Fetal Muscle Leg	muscle
19	chr19:38422000-38426400	Weak transcription	Primary T cells from cord blood	blood
20	chr19:38422200-38423400	Active TSS	A549	lung
21	chr19:38422200-38425000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr19:38422200-38425600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr19:38422400-38423000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr19:38422400-38423000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr19:38422400-38423000	Flanking Active TSS	Brain Germinal Matrix	brain
26	chr19:38422400-38423000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr19:38422400-38423200	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr19:38422400-38423200	Active TSS	Stomach Smooth Muscle	stomach
29	chr19:38422400-38423200	Active TSS	HepG2	liver
30	chr19:38422400-38423600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr19:38422400-38423600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr19:38422400-38423600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr19:38422400-38423600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr19:38422400-38423600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr19:38422400-38423600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:38422400-38423800	Flanking Active TSS	NHEK	skin
37	chr19:38422400-38424000	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr19:38422400-38424200	Flanking Active TSS	GM12878-XiMat	blood
39	chr19:38422400-38424400	Active TSS	Rectal Smooth Muscle	rectum
40	chr19:38422400-38424600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:38422400-38424800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr19:38422400-38424800	Enhancers	Left Ventricle	heart
43	chr19:38422400-38424800	Enhancers	HUVEC	blood vessel
44	chr19:38422400-38425000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:38422400-38425000	Enhancers	Psoas Muscle	Psoas
46	chr19:38422400-38425000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr19:38422600-38423000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:38422600-38423000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr19:38422600-38423000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr19:38422600-38423000	Active TSS	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links