Variant report

Variant	rs16942199
Chromosome Location	chr17:45764692-45764693
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:78)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:78 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:45764257-45765575	HCT-116	colon:	n/a	n/a
2	BCL3	chr17:45761066-45765975	A549	lung:	n/a	chr17:45762320-45762329 chr17:45761498-45761507
3	KAP1	chr17:45764278-45765542	U2OS	brain:	n/a	n/a
4	TEAD4	chr17:45764160-45764850	HepG2	liver:	n/a	n/a
5	SRF	chr17:45764377-45764724	HepG2	liver:	n/a	n/a
6	POLR2A	chr17:45763778-45764750	GM12878	blood:	n/a	n/a
7	POLR2A	chr17:45761123-45765686	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr17:45761016-45766013	HepG2	liver:	n/a	n/a
9	POLR2A	chr17:45764629-45764696	H1-hESC	embryonic stem cell:	n/a	n/a
10	MBD4	chr17:45764180-45764838	HepG2	liver:	n/a	n/a
11	POLR2A	chr17:45763735-45765619	MCF-7	breast:	n/a	n/a
12	POLR2A	chr17:45760728-45765897	A549	lung:	n/a	n/a
13	POLR2A	chr17:45760907-45765868	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr17:45760984-45765876	U87	brain:	n/a	n/a
15	CREB1	chr17:45764063-45764808	HepG2	liver:	n/a	n/a
16	CREB1	chr17:45764182-45764820	HepG2	liver:	n/a	n/a
17	POLR2A	chr17:45763805-45765611	GM12891	blood:	n/a	n/a
18	POLR2A	chr17:45760984-45765870	U87	brain:	n/a	n/a
19	POLR2A	chr17:45763842-45765946	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr17:45764057-45765856	U87	brain:	n/a	n/a
21	POLR2A	chr17:45758952-45766470	PANC-1	pancreas:	n/a	n/a
22	POLR2A	chr17:45764257-45765696	K562	blood:	n/a	n/a
23	POLR2A	chr17:45764092-45765784	HCT-116	colon:	n/a	n/a
24	POLR2A	chr17:45761050-45765590	HepG2	liver:	n/a	n/a
25	CEBPB	chr17:45763592-45764728	HepG2	liver:	n/a	chr17:45763751-45763762
26	POLR2A	chr17:45763522-45765856	U87	brain:	n/a	n/a
27	SRF	chr17:45764427-45764692	HepG2	liver:	n/a	n/a
28	FOSL2	chr17:45763845-45764699	HepG2	liver:	n/a	n/a
29	SP1	chr17:45764244-45764706	HepG2	liver:	n/a	n/a
30	RXRA	chr17:45764405-45764710	HepG2	liver:	n/a	n/a
31	POLR2A	chr17:45764254-45765709	HepG2	liver:	n/a	n/a
32	POLR2A	chr17:45763991-45765810	HepG2	liver:	n/a	n/a
33	POLR2A	chr17:45762680-45764943	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr17:45761025-45765803	GM12891	blood:	n/a	n/a
35	POLR2A	chr17:45763813-45764711	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr17:45763812-45764708	HepG2	liver:	n/a	n/a
37	POLR2A	chr17:45764661-45764930	GM12878	blood:	n/a	n/a
38	FOSL2	chr17:45763857-45764776	HepG2	liver:	n/a	n/a
39	TCF12	chr17:45764573-45765799	A549	lung:	n/a	n/a
40	POLR2A	chr17:45764389-45764810	GM12891	blood:	n/a	n/a
41	JUND	chr17:45764065-45764726	HepG2	liver:	n/a	n/a
42	NFATC1	chr17:45764045-45765713	GM12878	blood:	n/a	n/a
43	JUND	chr17:45764143-45765678	SK-N-SH	brain:	n/a	n/a
44	POLR2A	chr17:45760244-45765917	PFSK-1	brain:	n/a	n/a
45	FOXA2	chr17:45764274-45764718	HepG2	liver:	n/a	n/a
46	STAT5A	chr17:45763972-45765772	GM12878	blood:	n/a	chr17:45764590-45764602
47	POLR2A	chr17:45764380-45764712	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr17:45760907-45765675	GM12892	blood:	n/a	n/a
49	POLR2A	chr17:45764582-45765017	MCF10A-Er-Src	breast:	n/a	n/a
50	MTA3	chr17:45764051-45765740	GM12878	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45750704..45751981-chr17:45764009..45765030,12	MCF-7	breast:
2	chr17:45761397..45766819-chr17:45768713..45773362,9	K562	blood:
3	chr17:45764006..45765006-chr17:45774813..45775370,2	MCF-7	breast:
4	chr17:45751990..45755538-chr17:45760652..45765275,4	MCF-7	breast:
5	chr17:45758194..45759902-chr17:45762797..45765497,2	K562	blood:
6	chr17:45745574..45748775-chr17:45762933..45765883,3	K562	blood:
7	chr17:45752325..45755092-chr17:45763938..45765718,2	K562	blood:
8	chr17:45750858..45751981-chr17:45764122..45765029,9	MCF-7	breast:
9	chr17:45759177..45766275-chr17:45767435..45773662,12	K562	blood:
10	chr17:45750672..45751212-chr17:45764128..45764905,2	MCF-7	breast:
11	chr17:45763121..45767993-chr17:48940261..48944774,6	MCF-7	breast:
12	chr17:45763614..45766168-chr17:49023284..49025624,2	MCF-7	breast:
13	chr17:45751990..45754304-chr17:45764467..45767340,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000264558	TF binding region
ENSG00000141232	Chromatin interaction
ENSG00000108424	Chromatin interaction
ENSG00000198933	Chromatin interaction
ENSG00000229980	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11870935	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs2317826	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap]
rs3809868	1.00[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap]
rs4794047	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[ASN][1000 genomes]
rs4794048	1.00[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs7210738	1.00[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap]
rs8065669	1.00[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap]
rs8072100	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs8078686	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	esv1811231	chr17:45520374-45764956	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv1813964	chr17:45520374-45764956	Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv2758458	chr17:45520374-45764956	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv2758693	chr17:45520374-45764956	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv428344	chr17:45520374-45764956	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs16942199	SLC25A39	cis	parietal	SCAN
rs16942199	LOC653479	cis	multi-tissue	Pritchard
rs16942199	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs16942199	NPEPPS	cis	parietal	SCAN
rs16942199	C17orf57	cis	cerebellum	SCAN
rs16942199	MRPL45P2	cis	lymphoblastoid	seeQTL
rs16942199	KLHL10	cis	parietal	SCAN
rs16942199	VPS25	cis	parietal	SCAN
rs16942199	C17orf57	cis	parietal	SCAN
rs16942199	TBKBP1	cis	multi-tissue	Pritchard
rs16942199	DBF4B	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45728800-45765600	Strong transcription	Fetal Muscle Trunk	muscle
2	chr17:45730400-45764800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr17:45730400-45765000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:45733200-45765000	Strong transcription	HMEC	breast
5	chr17:45738400-45765600	Strong transcription	Primary T cells from cord blood	blood
6	chr17:45742000-45764800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr17:45752600-45765400	Strong transcription	Fetal Thymus	thymus
8	chr17:45753400-45765200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr17:45758200-45770200	Weak transcription	Fetal Heart	heart
10	chr17:45758200-45770600	Weak transcription	Fetal Brain Male	brain
11	chr17:45758400-45767400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr17:45759800-45767400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr17:45760000-45765200	Weak transcription	Stomach Mucosa	stomach
14	chr17:45760000-45769400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr17:45760200-45764800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr17:45760200-45769600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr17:45760200-45769600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr17:45760200-45770000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr17:45760200-45770000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr17:45760200-45770200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr17:45760400-45765000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr17:45760400-45765000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr17:45760400-45765200	Weak transcription	Ovary	ovary
24	chr17:45760400-45765200	Weak transcription	Spleen	Spleen
25	chr17:45760400-45766800	Weak transcription	Fetal Intestine Small	intestine
26	chr17:45760400-45768800	Weak transcription	Fetal Kidney	kidney
27	chr17:45760400-45769800	Weak transcription	Right Ventricle	heart
28	chr17:45760400-45770000	Weak transcription	Colonic Mucosa	Colon
29	chr17:45760400-45770000	Weak transcription	Pancreas	Pancrea
30	chr17:45760400-45770200	Weak transcription	Colon Smooth Muscle	Colon
31	chr17:45760400-45770400	Weak transcription	Gastric	stomach
32	chr17:45760400-45770400	Weak transcription	Hela-S3	cervix
33	chr17:45761000-45765400	Strong transcription	Fetal Brain Female	brain
34	chr17:45761200-45770000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr17:45761400-45764800	Strong transcription	Primary B cells from cord blood	blood
36	chr17:45761400-45764800	Genic enhancers	HUVEC	blood vessel
37	chr17:45761400-45764800	Genic enhancers	Osteobl	bone
38	chr17:45761600-45765600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr17:45761600-45765800	Strong transcription	Brain Germinal Matrix	brain
40	chr17:45761600-45769800	Weak transcription	Esophagus	oesophagus
41	chr17:45762000-45769400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr17:45762200-45764800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr17:45762200-45765000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr17:45762200-45765600	Enhancers	NHLF	lung
45	chr17:45762200-45770200	Weak transcription	Small Intestine	intestine
46	chr17:45762200-45770400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr17:45762400-45764800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr17:45762400-45764800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr17:45762400-45764800	Weak transcription	Brain Substantia Nigra	brain
50	chr17:45762400-45764800	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links