Variant report

Variant	rs196686
Chromosome Location	chr6:80129933-80129934
allele	A/C
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	USF1	chr6:80129724-80130031	K562	blood:	n/a	chr6:80129901-80129912
2	USF1	chr6:80129704-80130029	SK-N-SH_RA	brain:	n/a	chr6:80129901-80129912
3	USF1	chr6:80129789-80130070	A549	lung:	n/a	chr6:80129901-80129912
4	USF1	chr6:80129618-80130154	H1-hESC	embryonic stem cell:	n/a	chr6:80129901-80129912
5	SIX5	chr6:80129806-80129948	K562	blood:	n/a	n/a
6	BATF	chr6:80129774-80129974	GM12878	blood:	n/a	n/a
7	USF1	chr6:80129680-80130005	H1-hESC	embryonic stem cell:	n/a	chr6:80129901-80129912
8	SIX5	chr6:80129744-80130039	GM12878	blood:	n/a	n/a
9	ATF3	chr6:80129686-80129975	GM12878	blood:	n/a	n/a
10	USF1	chr6:80129596-80130245	HCT-116	colon:	n/a	chr6:80129901-80129912
11	SIX5	chr6:80129670-80130001	GM12878	blood:	n/a	n/a
12	USF1	chr6:80129665-80130159	ECC-1	luminal epithelium:	n/a	chr6:80129901-80129912
13	BATF	chr6:80129819-80129980	GM12878	blood:	n/a	n/a
14	USF2	chr6:80129739-80130107	Hela-S3	cervix:	n/a	chr6:80129901-80129912
15	USF1	chr6:80129680-80130091	A549	lung:	n/a	chr6:80129901-80129912
16	USF1	chr6:80129678-80130089	SK-N-SH	brain:	n/a	chr6:80129901-80129912
17	USF1	chr6:80129783-80130018	HepG2	liver:	n/a	chr6:80129901-80129912
18	USF1	chr6:80129684-80130088	SK-N-SH_RA	brain:	n/a	chr6:80129901-80129912
19	USF1	chr6:80129684-80130162	HCT-116	colon:	n/a	chr6:80129901-80129912
20	SIX5	chr6:80129706-80130089	H1-hESC	embryonic stem cell:	n/a	n/a
21	USF2	chr6:80129741-80130076	GM12878	blood:	n/a	chr6:80129901-80129912
22	YY1	chr6:80129784-80129999	SK-N-SH_RA	brain:	n/a	n/a
23	HCFC1	chr6:80129702-80130084	K562	blood:	n/a	n/a
24	NRF1	chr6:80129866-80129985	GM12878	blood:	n/a	n/a
25	USF1	chr6:80129585-80130205	ECC-1	luminal epithelium:	n/a	chr6:80129901-80129912
26	USF2	chr6:80129749-80130053	H1-hESC	embryonic stem cell:	n/a	chr6:80129901-80129912
27	USF1	chr6:80129757-80129977	A549	lung:	n/a	chr6:80129901-80129912
28	USF1	chr6:80129680-80130057	K562	blood:	n/a	chr6:80129901-80129912
29	ZNF143	chr6:80129719-80130085	GM12878	blood:	n/a	n/a
30	ZNF143	chr6:80129717-80130067	K562	blood:	n/a	n/a
31	ZNF143	chr6:80129736-80130026	Hela-S3	cervix:	n/a	n/a
32	ZNF143	chr6:80129722-80130071	H1-hESC	embryonic stem cell:	n/a	n/a
33	USF1	chr6:80129756-80129970	A549	lung:	n/a	chr6:80129901-80129912
34	USF1	chr6:80129782-80129998	HepG2	liver:	n/a	chr6:80129901-80129912
35	YY1	chr6:80129659-80130008	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SH3BGRL2-2	chr6:80129867-80130154	NONHSAT113689

Variant related genes	Relation type
ENSG00000231533	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs196675	0.82[EUR][1000 genomes]
rs196687	0.91[ASN][1000 genomes]
rs196688	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs196691	0.82[EUR][1000 genomes]
rs196693	0.97[EUR][1000 genomes]
rs3843505	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846736	0.86[EUR][1000 genomes]
rs3846738	0.95[EUR][1000 genomes]
rs3912466	0.99[ASN][1000 genomes]
rs473594	0.93[EUR][1000 genomes]
rs6454121	0.89[EUR][1000 genomes]
rs7773764	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv886301	chr6:80111104-80339088	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv886302	chr6:80111104-80355973	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1030126	chr6:80113449-80209165	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1027388	chr6:80113449-80355973	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80116200-80131600	Weak transcription	Fetal Intestine Small	intestine
2	chr6:80123600-80131800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:80123800-80130200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:80126400-80131400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr6:80129000-80130000	Weak transcription	Fetal Lung	lung
6	chr6:80129200-80130000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:80129400-80130000	Enhancers	Primary hematopoietic stem cells	blood
8	chr6:80129400-80130600	Flanking Active TSS	Dnd41	blood
9	chr6:80129600-80130000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
10	chr6:80129600-80130200	Active TSS	Brain Cingulate Gyrus	brain
11	chr6:80129600-80130400	Active TSS	Brain Hippocampus Middle	brain
12	chr6:80129600-80131000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:80129800-80130000	Flanking Active TSS	Brain Angular Gyrus	brain
14	chr6:80129800-80130000	Flanking Active TSS	Brain Substantia Nigra	brain
15	chr6:80129800-80130200	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr6:80129800-80130600	Enhancers	Placenta	Placenta
17	chr6:80129800-80130800	Active TSS	Brain Anterior Caudate	brain
18	chr6:80129800-80130800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:80129800-80131200	Enhancers	NHLF	lung
20	chr6:80129800-80131600	Enhancers	HUVEC	blood vessel
21	chr6:80129800-80133200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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