Variant report

Variant	rs16955658
Chromosome Location	chr15:29968438-29968439
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	E2F6	chr15:29966729-29968510	A549	lung:	n/a	chr15:29968271-29968283 chr15:29968272-29968279 chr15:29968272-29968279 chr15:29967212-29967222 chr15:29968271-29968280 chr15:29968272-29968279
2	POLR2A	chr15:29968028-29968473	A549	lung:	n/a	n/a
3	MAX	chr15:29966665-29968613	A549	lung:	n/a	chr15:29967029-29967039
4	POLR2A	chr15:29966921-29968466	A549	lung:	n/a	n/a
5	NFIC	chr15:29967998-29968607	ECC-1	luminal epithelium:	n/a	n/a
6	SP1	chr15:29968123-29968482	H1-hESC	embryonic stem cell:	n/a	chr15:29968136-29968150 chr15:29968371-29968385
7	NFIC	chr15:29968046-29968755	ECC-1	luminal epithelium:	n/a	n/a
8	E2F6	chr15:29967651-29968476	H1-hESC	embryonic stem cell:	n/a	chr15:29968271-29968283 chr15:29968272-29968279 chr15:29968272-29968279 chr15:29968271-29968280 chr15:29968272-29968279
9	E2F6	chr15:29966958-29968566	H1-hESC	embryonic stem cell:	n/a	chr15:29968271-29968283 chr15:29968272-29968279 chr15:29968272-29968279 chr15:29967212-29967222 chr15:29968271-29968280 chr15:29968272-29968279
10	SP1	chr15:29966668-29968561	A549	lung:	n/a	chr15:29967121-29967132 chr15:29967201-29967210 chr15:29968136-29968150 chr15:29967199-29967211 chr15:29967381-29967395 chr15:29966994-29967003 chr15:29968371-29968385
11	PBX3	chr15:29967634-29968487	A549	lung:	n/a	n/a
12	POLR2A	chr15:29966914-29968445	A549	lung:	n/a	n/a
13	TCF12	chr15:29967959-29968641	ECC-1	luminal epithelium:	n/a	n/a
14	EP300	chr15:29968095-29968616	ECC-1	luminal epithelium:	n/a	chr15:29968292-29968302
15	TCF12	chr15:29966112-29968615	A549	lung:	n/a	n/a
16	BCL3	chr15:29968046-29968574	A549	lung:	n/a	chr15:29968268-29968277 chr15:29968175-29968188
17	TAF1	chr15:29966644-29968491	A549	lung:	n/a	n/a
18	TCF12	chr15:29967933-29968708	ECC-1	luminal epithelium:	n/a	n/a
19	JUND	chr15:29966782-29968526	A549	lung:	n/a	n/a
20	FOXA2	chr15:29968017-29968635	A549	lung:	n/a	chr15:29968293-29968305
21	EP300	chr15:29967868-29968703	ECC-1	luminal epithelium:	n/a	chr15:29968292-29968302
22	MAX	chr15:29966679-29968537	A549	lung:	n/a	chr15:29967029-29967039

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:29961960..29963805-chr15:29967307..29968997,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256802	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11854637	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16955661	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456736	chr15:29327352-30208654	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv568675	chr15:29327352-30208654	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv903747	chr15:29361126-30008977	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv995038	chr15:29744279-30366124	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1038495	chr15:29825859-30351687	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv542293	chr15:29825859-30351687	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv832944	chr15:29861062-30082057	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv832945	chr15:29932599-30123721	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16955658	TJP1	cis	lymphoblastoid	seeQTL
rs16955658	ASRGL1	trans	lymphoblastoid	seeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:29965000-29969000	Weak transcription	Fetal Lung	lung
2	chr15:29965600-29969800	Enhancers	Fetal Brain Male	brain
3	chr15:29966400-29968600	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr15:29966400-29968600	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr15:29966400-29968600	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr15:29966600-29968600	Active TSS	H9 Cell Line	embryonic stem cell
7	chr15:29966600-29968600	Active TSS	Fetal Intestine Large	intestine
8	chr15:29966600-29968600	Active TSS	Fetal Intestine Small	intestine
9	chr15:29966600-29969200	Active TSS	Duodenum Mucosa	Duodenum
10	chr15:29966800-29968600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr15:29967000-29968600	Active TSS	Pancreas	Pancrea
12	chr15:29967200-29971400	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr15:29967600-29969000	Weak transcription	HSMMtube	muscle
14	chr15:29967600-29969600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr15:29967800-29969600	Weak transcription	Brain Angular Gyrus	brain
16	chr15:29967800-29969800	Weak transcription	Colonic Mucosa	Colon
17	chr15:29967800-29969800	Weak transcription	Lung	lung
18	chr15:29967800-29970000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:29967800-29970200	Weak transcription	Right Atrium	heart
20	chr15:29967800-29970400	Weak transcription	Brain Substantia Nigra	brain
21	chr15:29968000-29968600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
22	chr15:29968000-29968800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr15:29968000-29969000	Weak transcription	NHDF-Ad	bronchial
24	chr15:29968000-29969400	Weak transcription	Brain Hippocampus Middle	brain
25	chr15:29968000-29970400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:29968000-29970600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:29968000-29971000	Transcr. at gene 5' and 3'	A549	lung
28	chr15:29968000-29977400	Weak transcription	NHLF	lung
29	chr15:29968200-29968600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr15:29968200-29968600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr15:29968200-29968600	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr15:29968200-29969000	Weak transcription	HSMM	muscle
33	chr15:29968200-29969200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr15:29968200-29969600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr15:29968200-29969600	Enhancers	Brain Germinal Matrix	brain
36	chr15:29968200-29969600	Weak transcription	Right Ventricle	heart
37	chr15:29968200-29970200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:29968200-29970200	Weak transcription	Fetal Heart	heart
39	chr15:29968200-29970200	Weak transcription	Spleen	Spleen
40	chr15:29968200-29970600	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr15:29968200-29974200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr15:29968400-29968600	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr15:29968400-29968600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr15:29968400-29968600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:29968400-29968600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr15:29968400-29968600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:29968400-29968600	Enhancers	Liver	Liver
48	chr15:29968400-29968600	Bivalent Enhancer	Fetal Stomach	stomach
49	chr15:29968400-29968600	Weak transcription	Stomach Mucosa	stomach
50	chr15:29968400-29968800	Weak transcription	HUVEC	blood vessel

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