Variant report

Variant	rs4653437
Chromosome Location	chr1:226078915-226078916
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	ELF1	chr1:226078592-226078944	K562	blood:	n/a	chr1:226078791-226078802 chr1:226078789-226078802
2	FOXA1	chr1:226078717-226079242	HepG2	liver:	n/a	n/a
3	EP300	chr1:226078877-226079055	HepG2	liver:	n/a	n/a
4	FOXA1	chr1:226078813-226079195	HepG2	liver:	n/a	n/a
5	NR3C1	chr1:226078568-226079184	A549	lung:	n/a	chr1:226078787-226078803 chr1:226078787-226078803 chr1:226078782-226078808 chr1:226078788-226078802 chr1:226078782-226078808 chr1:226078972-226078986 chr1:226078786-226078804 chr1:226078782-226078808
6	EP300	chr1:226078673-226079428	ECC-1	luminal epithelium:	n/a	chr1:226078791-226078800
7	FOXA1	chr1:226078808-226079144	A549	lung:	n/a	n/a
8	NR3C1	chr1:226078707-226079091	A549	lung:	n/a	chr1:226078787-226078803 chr1:226078787-226078803 chr1:226078782-226078808 chr1:226078788-226078802 chr1:226078782-226078808 chr1:226078972-226078986 chr1:226078786-226078804 chr1:226078782-226078808
9	NR3C1	chr1:226078621-226079267	ECC-1	luminal epithelium:	n/a	chr1:226078787-226078803 chr1:226078787-226078803 chr1:226078782-226078808 chr1:226078788-226078802 chr1:226078782-226078808 chr1:226078972-226078986 chr1:226078786-226078804 chr1:226078782-226078808
10	TCF12	chr1:226078641-226079251	ECC-1	luminal epithelium:	n/a	chr1:226078688-226078695
11	FOXA1	chr1:226078806-226079272	HepG2	liver:	n/a	n/a
12	TEAD4	chr1:226078787-226079342	HepG2	liver:	n/a	n/a
13	MYBL2	chr1:226078724-226079294	HepG2	liver:	n/a	n/a
14	NR3C1	chr1:226078568-226079316	ECC-1	luminal epithelium:	n/a	chr1:226078787-226078803 chr1:226078787-226078803 chr1:226078782-226078808 chr1:226078788-226078802 chr1:226078782-226078808 chr1:226078972-226078986 chr1:226078786-226078804 chr1:226078782-226078808
15	NR3C1	chr1:226078643-226079255	A549	lung:	n/a	chr1:226078787-226078803 chr1:226078787-226078803 chr1:226078782-226078808 chr1:226078788-226078802 chr1:226078782-226078808 chr1:226078972-226078986 chr1:226078786-226078804 chr1:226078782-226078808
16	FOXA2	chr1:226078811-226079202	HepG2	liver:	n/a	n/a
17	CREB1	chr1:226078119-226079208	HepG2	liver:	n/a	chr1:226078541-226078554
18	FOXA1	chr1:226078855-226079159	A549	lung:	n/a	n/a
19	NR3C1	chr1:226078851-226079143	A549	lung:	n/a	chr1:226078972-226078986
20	HNF4G	chr1:226078860-226079162	HepG2	liver:	n/a	n/a
21	NR2F2	chr1:226077982-226079607	HepG2	liver:	n/a	n/a
22	EP300	chr1:226078747-226079292	HepG2	liver:	n/a	chr1:226078791-226078800
23	ZBTB7A	chr1:226078887-226079075	HepG2	liver:	n/a	n/a
24	NR3C1	chr1:226078486-226079258	A549	lung:	n/a	chr1:226078787-226078803 chr1:226078787-226078803 chr1:226078782-226078808 chr1:226078788-226078802 chr1:226078782-226078808 chr1:226078972-226078986 chr1:226078786-226078804 chr1:226078782-226078808
25	HDAC2	chr1:226078848-226079191	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:226078420..226080294-chr1:226109083..226112006,2	MCF-7	breast:
2	chr1:226068530..226073051-chr1:226075073..226079547,5	MCF-7	breast:

Variant related genes	Relation type
LEFTY1	TF binding region
ENSG00000143811	Chromatin interaction
ENSG00000196187	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1877726	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3753668	0.81[YRI][hapmap]
rs3766941	0.81[YRI][hapmap]
rs3806259	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3820238	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv520628	chr1:226026406-226093362	Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	esv3335650	chr1:226074720-226125458	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	esv3369235	chr1:226075748-226127738	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv468216	chr1:226078915-226135132	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv549267	chr1:226078915-226135132	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4653437	PSEN2	cis	lymphoblastoid	seeQTL
rs4653437	NVL	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226071000-226083600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:226072000-226081200	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr1:226072000-226081600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:226072000-226082000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr1:226073200-226079800	Enhancers	Liver	Liver
6	chr1:226075400-226079200	Enhancers	Ovary	ovary
7	chr1:226075800-226079000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:226076200-226079000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:226076400-226079000	Enhancers	Placenta	Placenta
10	chr1:226076600-226079000	Enhancers	Fetal Intestine Small	intestine
11	chr1:226076600-226079800	Enhancers	Stomach Mucosa	stomach
12	chr1:226076600-226080400	Enhancers	Pancreas	Pancrea
13	chr1:226076800-226079000	Enhancers	Fetal Lung	lung
14	chr1:226076800-226079600	Enhancers	Fetal Intestine Large	intestine
15	chr1:226076800-226079800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:226076800-226079800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:226076800-226079800	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr1:226076800-226084600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:226077000-226079200	Enhancers	H9 Cell Line	embryonic stem cell
20	chr1:226077000-226085200	Weak transcription	Spleen	Spleen
21	chr1:226077000-226099000	Weak transcription	Right Atrium	heart
22	chr1:226077200-226079000	Enhancers	Colonic Mucosa	Colon
23	chr1:226077200-226079200	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr1:226077400-226079200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr1:226077400-226079600	Enhancers	Duodenum Mucosa	Duodenum
26	chr1:226077400-226079800	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr1:226077400-226079800	Flanking Active TSS	HepG2	liver
28	chr1:226077400-226084600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:226077600-226079200	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr1:226077600-226079400	Enhancers	H1 Cell Line	embryonic stem cell
31	chr1:226077800-226079200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:226077800-226079800	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr1:226078000-226079000	Weak transcription	Fetal Kidney	kidney
34	chr1:226078000-226080400	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr1:226078200-226079000	Weak transcription	Small Intestine	intestine
36	chr1:226078200-226079800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:226078200-226079800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:226078200-226079800	Enhancers	Gastric	stomach
39	chr1:226078200-226079800	Enhancers	HMEC	breast
40	chr1:226078200-226080400	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr1:226078400-226079000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:226078400-226079000	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr1:226078400-226079000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr1:226078400-226079000	Enhancers	Primary T cells fromperipheralblood	blood
45	chr1:226078400-226079000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr1:226078400-226079200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:226078400-226079800	Enhancers	Hela-S3	cervix
48	chr1:226078600-226079200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr1:226078600-226079200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr1:226078600-226084000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links