Variant report

Variant	rs6968392
Chromosome Location	chr7:5184234-5184235
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	CHD2	chr7:5184054-5184470	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:5183857-5184552	GM12878	blood:	n/a	n/a
3	USF1	chr7:5184122-5184492	K562	blood:	n/a	chr7:5184349-5184360
4	POU2F2	chr7:5184033-5184521	GM12891	blood:	n/a	n/a
5	USF1	chr7:5184121-5184429	A549	lung:	n/a	chr7:5184349-5184360
6	ELF1	chr7:5183599-5184599	GM12878	blood:	n/a	chr7:5184206-5184219
7	YY1	chr7:5184038-5184557	GM12891	blood:	n/a	n/a
8	YY1	chr7:5183976-5184547	GM12878	blood:	n/a	n/a
9	YY1	chr7:5183988-5184546	GM12891	blood:	n/a	n/a
10	YY1	chr7:5184128-5184479	H1-hESC	embryonic stem cell:	n/a	n/a
11	RUNX3	chr7:5184043-5184463	GM12878	blood:	n/a	n/a
12	IRF4	chr7:5184052-5184546	GM12878	blood:	n/a	n/a
13	SIX5	chr7:5184176-5184349	K562	blood:	n/a	chr7:5184273-5184282 chr7:5184271-5184280
14	TBL1XR1	chr7:5183828-5184448	GM12878	blood:	n/a	n/a
15	EBF1	chr7:5183535-5184473	GM12878	blood:	n/a	chr7:5183737-5183748 chr7:5184260-5184273
16	ZNF143	chr7:5184176-5184438	H1-hESC	embryonic stem cell:	n/a	chr7:5184271-5184280 chr7:5184271-5184289 chr7:5184273-5184282
17	ZNF143	chr7:5184061-5184510	GM12878	blood:	n/a	chr7:5184271-5184280 chr7:5184271-5184289 chr7:5184434-5184443 chr7:5184273-5184282
18	ELF1	chr7:5183970-5184470	K562	blood:	n/a	chr7:5184206-5184219
19	USF1	chr7:5184082-5184404	A549	lung:	n/a	chr7:5184349-5184360
20	POLR2A	chr7:5183998-5184498	SK-N-MC	brain:	n/a	n/a
21	MAX	chr7:5183946-5184565	K562	blood:	n/a	chr7:5184462-5184478 chr7:5184191-5184200 chr7:5184187-5184196 chr7:5184469-5184478
22	PAX5	chr7:5183947-5184539	GM12878	blood:	n/a	n/a
23	STAT1	chr7:5184115-5184315	GM12878	blood:	n/a	n/a
24	POLR2A	chr7:5184154-5184238	MCF-7	breast:	n/a	n/a
25	GABPA	chr7:5183979-5184401	K562	blood:	n/a	n/a
26	POLR2A	chr7:5184077-5184513	GM12891	blood:	n/a	n/a
27	SPI1	chr7:5184020-5184353	GM12891	blood:	n/a	n/a
28	USF1	chr7:5184180-5184439	H1-hESC	embryonic stem cell:	n/a	chr7:5184349-5184360
29	ETS1	chr7:5183985-5184480	GM12878	blood:	n/a	chr7:5184211-5184221 chr7:5184210-5184219 chr7:5184270-5184283 chr7:5184274-5184281 chr7:5184269-5184282 chr7:5184210-5184219
30	YY1	chr7:5184150-5184459	K562	blood:	n/a	n/a
31	PAX5	chr7:5184089-5184260	GM12878	blood:	n/a	n/a
32	YY1	chr7:5184169-5184406	GM12892	blood:	n/a	n/a
33	GABPA	chr7:5184097-5184408	Hela-S3	cervix:	n/a	n/a
34	GABPA	chr7:5184023-5184257	HepG2	liver:	n/a	n/a
35	FOXM1	chr7:5184041-5184426	GM12878	blood:	n/a	n/a
36	USF2	chr7:5183988-5184546	GM12878	blood:	n/a	n/a
37	MXI1	chr7:5183729-5184533	GM12878	blood:	n/a	chr7:5184187-5184202 chr7:5184472-5184481
38	BHLHE40	chr7:5183971-5184469	GM12878	blood:	n/a	n/a
39	ZEB1	chr7:5184030-5184338	GM12878	blood:	n/a	n/a
40	USF1	chr7:5184037-5184465	GM12878	blood:	n/a	chr7:5184349-5184360
41	SP1	chr7:5183613-5184515	GM12878	blood:	n/a	n/a
42	GABPA	chr7:5184046-5184399	GM12878	blood:	n/a	n/a
43	HCFC1	chr7:5184105-5184459	K562	blood:	n/a	n/a
44	SIN3A	chr7:5183749-5184528	GM12878	blood:	n/a	n/a
45	PAX5	chr7:5184050-5184444	GM12878	blood:	n/a	n/a
46	ZNF143	chr7:5184139-5184467	K562	blood:	n/a	chr7:5184271-5184280 chr7:5184271-5184289 chr7:5184434-5184443 chr7:5184273-5184282
47	EP300	chr7:5184031-5184478	GM12878	blood:	n/a	chr7:5184211-5184218
48	POLR2A	chr7:5183964-5184261	GM12878	blood:	n/a	n/a
49	MAZ	chr7:5183654-5184495	GM12878	blood:	n/a	chr7:5184462-5184478 chr7:5184191-5184200 chr7:5184187-5184196 chr7:5184469-5184478
50	SIX5	chr7:5184067-5184399	GM12878	blood:	n/a	chr7:5184273-5184282 chr7:5184271-5184280

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:5184212..5184729-chr7:5862163..5863064,2	MCF-7	breast:

Variant related genes	Relation type
ZNF890P	TF binding region
ENSG00000235944	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10951818	0.80[EUR][1000 genomes]
rs11765350	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11768814	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12671440	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12672204	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56054124	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56325633	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61547825	0.80[EUR][1000 genomes]
rs62442011	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6943365	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6946651	0.83[EUR][1000 genomes]
rs7808305	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs888584	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530968	chr7:4572250-5418004	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1031697	chr7:4677463-5241790	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv538704	chr7:4677463-5241790	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
5	nsv1029430	chr7:5053887-5223583	Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1032880	chr7:5066181-5205932	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1030384	chr7:5066181-5210555	Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
9	nsv1031007	chr7:5101766-5262695	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv916396	chr7:5128917-5370805	Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv1027026	chr7:5132597-5188557	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv605982	chr7:5133219-5222956	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv523630	chr7:5144105-5198328	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
15	nsv433016	chr7:5157617-5215853	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	esv2762643	chr7:5172994-5216265	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6968392	PMS2	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5182800-5184600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr7:5183400-5184400	Enhancers	Primary B cells from cord blood	blood
3	chr7:5183400-5184400	Active TSS	Brain Cingulate Gyrus	brain
4	chr7:5183400-5184400	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr7:5183400-5184400	Active TSS	Hela-S3	cervix
6	chr7:5183800-5184400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr7:5183800-5184400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr7:5183800-5184400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr7:5183800-5184400	Enhancers	Spleen	Spleen
10	chr7:5183800-5184600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr7:5183800-5184600	Flanking Active TSS	GM12878-XiMat	blood
12	chr7:5184000-5184400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:5184000-5184400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr7:5184000-5184400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr7:5184000-5184400	Active TSS	Brain Angular Gyrus	brain
16	chr7:5184000-5184400	Active TSS	Brain Germinal Matrix	brain
17	chr7:5184000-5184400	Enhancers	Esophagus	oesophagus
18	chr7:5184000-5184400	Enhancers	Placenta	Placenta
19	chr7:5184000-5184400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
20	chr7:5184000-5184400	Flanking Active TSS	HMEC	breast
21	chr7:5184000-5184400	Active TSS	HSMM	muscle
22	chr7:5184000-5184400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
23	chr7:5184000-5184400	Active TSS	NH-A	brain
24	chr7:5184000-5184600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr7:5184000-5184600	Enhancers	Fetal Brain Male	brain
26	chr7:5184000-5184600	Enhancers	K562	blood
27	chr7:5184200-5184400	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr7:5184200-5184400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr7:5184200-5184400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr7:5184200-5184400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr7:5184200-5184400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr7:5184200-5184400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr7:5184200-5184400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr7:5184200-5184400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
35	chr7:5184200-5184400	Active TSS	Fetal Brain Female	brain
36	chr7:5184200-5184400	Bivalent Enhancer	Fetal Lung	lung
37	chr7:5184200-5184600	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr7:5184200-5184600	Enhancers	Primary B cells from peripheral blood	blood
39	chr7:5184200-5184600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
40	chr7:5184200-5184600	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr7:5184200-5184600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr7:5184200-5184600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr7:5184200-5184600	Enhancers	Fetal Thymus	thymus

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