Variant report

Variant	rs39771
Chromosome Location	chr8:90838606-90838607
allele	C/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	RELA	chr8:90838281-90838940	GM18951	blood:	n/a	chr8:90838593-90838602 chr8:90838593-90838602
2	FOXA1	chr8:90838495-90838856	HepG2	liver:	n/a	n/a
3	ZNF384	chr8:90838102-90838802	K562	blood:	n/a	n/a
4	RELA	chr8:90838199-90839365	GM12891	blood:	n/a	chr8:90838593-90838602 chr8:90838593-90838602
5	RUNX3	chr8:90838278-90838806	GM12878	blood:	n/a	n/a
6	JUND	chr8:90838406-90838792	K562	blood:	n/a	n/a
7	EP300	chr8:90838518-90838653	GM12878	blood:	n/a	n/a
8	MAFF	chr8:90838489-90838653	K562	blood:	n/a	n/a
9	BHLHE40	chr8:90838425-90838937	GM12878	blood:	n/a	n/a
10	FOXA2	chr8:90838518-90838932	A549	lung:	n/a	n/a
11	POLR2A	chr8:90837963-90838752	U87	brain:	n/a	n/a
12	ZNF384	chr8:90838152-90838868	GM12878	blood:	n/a	n/a
13	NFIC	chr8:90838327-90839043	GM12878	blood:	n/a	chr8:90838955-90838971 chr8:90838955-90838972
14	GATA3	chr8:90838161-90839200	SK-N-SH	brain:	n/a	chr8:90838470-90838480
15	RCOR1	chr8:90838268-90838864	K562	blood:	n/a	n/a
16	RELA	chr8:90838334-90838923	GM19099	blood:	n/a	chr8:90838593-90838602 chr8:90838593-90838602
17	EBF1	chr8:90838506-90838940	GM12878	blood:	n/a	chr8:90838835-90838846
18	TCF12	chr8:90838026-90839203	SK-N-SH	brain:	n/a	chr8:90838761-90838770
19	POLR2A	chr8:90837963-90838633	U87	brain:	n/a	n/a
20	WRNIP1	chr8:90838229-90838890	GM12878	blood:	n/a	n/a
21	RELA	chr8:90838121-90838982	GM12878	blood:	n/a	chr8:90838593-90838602 chr8:90838593-90838602
22	FOXA2	chr8:90838522-90839106	A549	lung:	n/a	n/a
23	RFX5	chr8:90837585-90838692	IMR90	lung:	n/a	n/a
24	CHD2	chr8:90838378-90838823	GM12878	blood:	n/a	n/a
25	EP300	chr8:90838176-90838632	GM12878	blood:	n/a	chr8:90838472-90838481 chr8:90838468-90838482

No.	Distal block	Cell Line	Cell type
1	chr8:90838601..90840941-chr8:90843850..90846321,2	MCF-7	breast:
2	chr8:90824515..90827081-chr8:90836313..90840458,3	MCF-7	breast:
3	chr8:90835454..90837187-chr8:90837338..90840296,2	MCF-7	breast:
4	chr8:90838578..90843611-chr8:90912392..90915640,4	MCF-7	breast:
5	chr8:90836699..90839189-chr8:90853198..90855476,2	MCF-7	breast:
6	chr8:90838136..90841638-chr8:90842560..90845111,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NBN-5	chr8:90838399-90839074	ucscGeneNc_uc003yed_1

Variant related genes	Relation type
COX6B1P6	TF binding region
ENSG00000164823	Chromatin interaction
ENSG00000253349	Chromatin interaction
ENSG00000207359	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10094579	0.81[ASN][1000 genomes]
rs12155807	0.81[ASN][1000 genomes]
rs13278954	0.81[ASN][1000 genomes]
rs16901016	0.81[ASN][1000 genomes]
rs28144	0.82[AFR][1000 genomes]
rs28766093	0.81[ASN][1000 genomes]
rs34642426	0.81[ASN][1000 genomes]
rs35183880	0.81[ASN][1000 genomes]
rs365871	0.93[ASN][1000 genomes]
rs369771	0.89[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs374957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs376110	0.97[AFR][1000 genomes]
rs386857	0.90[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs394108	0.84[JPT][hapmap];0.89[YRI][hapmap]
rs39515	0.84[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs39519	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs39772	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs398959	0.92[ASN][1000 genomes]
rs400571	0.90[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs40250	0.94[EUR][1000 genomes]
rs40457	0.97[AFR][1000 genomes]
rs40459	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs40637	0.82[AFR][1000 genomes]
rs410577	0.90[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs410663	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs418634	0.90[EUR][1000 genomes]
rs419890	0.94[EUR][1000 genomes]
rs42186	0.93[EUR][1000 genomes]
rs42481	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs425312	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs426240	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs427854	0.92[EUR][1000 genomes]
rs43136	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs43227	0.97[AFR][1000 genomes]
rs43229	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs438485	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs447989	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs453266	0.97[AFR][1000 genomes]
rs454561	0.89[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs6984540	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv891182	chr8:90785685-90888786	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv520356	chr8:90823687-90857989	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv968495	chr8:90835687-90842298	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv2761448	chr8:90837630-90853986	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs39771	RP11-37B2.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90828000-90845800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr8:90836800-90839000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr8:90837000-90839000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr8:90837000-90847600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr8:90837200-90844600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr8:90837600-90839200	Enhancers	Muscle Satellite Cultured Cells	--
7	chr8:90837800-90839000	Weak transcription	HepG2	liver
8	chr8:90837800-90839200	Enhancers	GM12878-XiMat	blood
9	chr8:90837800-90839200	Enhancers	Osteobl	bone
10	chr8:90838000-90839000	Enhancers	Stomach Mucosa	stomach
11	chr8:90838000-90839600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr8:90838000-90841000	Enhancers	NHDF-Ad	bronchial
13	chr8:90838200-90839000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr8:90838200-90839000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr8:90838200-90839000	Flanking Active TSS	A549	lung
16	chr8:90838200-90839000	Enhancers	NH-A	brain
17	chr8:90838400-90838800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr8:90838400-90839000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr8:90838400-90839000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr8:90838600-90841000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links