Variant report

Variant	rs4959039
Chromosome Location	chr6:29957069-29957070
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	GATA3	chr6:29956973-29957478	SK-N-SH	brain:	n/a	n/a
2	STAT3	chr6:29957034-29957392	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:29956108..29958898-chr6:29958953..29961030,2	K562	blood:
2	chr6:29949567..29952384-chr6:29955471..29958344,3	K562	blood:
3	chr6:29955944..29957540-chr6:29961326..29963329,2	K562	blood:
4	chr6:29949567..29951883-chr6:29956360..29958897,2	K562	blood:

Variant related genes	Relation type
DDX39BP2	TF binding region
ENSG00000224312	Chromatin interaction
ENSG00000238024	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10947050	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11752303	0.88[EUR][1000 genomes]
rs12193100	0.84[EUR][1000 genomes]
rs12193110	0.81[EUR][1000 genomes]
rs12195207	0.86[EUR][1000 genomes]
rs12195260	0.87[EUR][1000 genomes]
rs12200084	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12202241	0.87[EUR][1000 genomes]
rs12206499	0.85[EUR][1000 genomes]
rs2071568	0.89[EUR][1000 genomes]
rs2275855	0.93[EUR][1000 genomes]
rs2394247	0.81[EUR][1000 genomes]
rs2508035	0.84[EUR][1000 genomes]
rs2523935	0.82[EUR][1000 genomes]
rs35066870	0.88[EUR][1000 genomes]
rs35159526	0.88[EUR][1000 genomes]
rs3823352	0.87[EUR][1000 genomes]
rs3823353	0.86[EUR][1000 genomes]
rs3823354	0.87[EUR][1000 genomes]
rs3823355	0.87[EUR][1000 genomes]
rs3823358	0.87[EUR][1000 genomes]
rs3823369	0.88[EUR][1000 genomes]
rs3910312	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4248141	0.81[EUR][1000 genomes]
rs4248142	0.81[EUR][1000 genomes]
rs4248143	0.81[EUR][1000 genomes]
rs4711206	0.93[EUR][1000 genomes]
rs4711207	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4711209	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4713269	0.81[EUR][1000 genomes]
rs4713270	0.81[EUR][1000 genomes]
rs4713274	0.89[EUR][1000 genomes]
rs4713275	0.86[EUR][1000 genomes]
rs4713279	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4713281	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4947244	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4959010	0.89[EUR][1000 genomes]
rs4959038	0.81[EUR][1000 genomes]
rs4959040	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6457127	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6903753	0.89[EUR][1000 genomes]
rs6904029	0.89[EUR][1000 genomes]
rs6916422	0.86[EUR][1000 genomes]
rs6916451	0.86[EUR][1000 genomes]
rs6935024	0.81[EUR][1000 genomes]
rs7766469	0.93[EUR][1000 genomes]
rs9295825	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9295826	0.92[EUR][1000 genomes]
rs9295829	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9348835	0.93[EUR][1000 genomes]
rs9357088	0.84[EUR][1000 genomes]
rs9357092	0.93[EUR][1000 genomes]
rs9366750	0.93[EUR][1000 genomes]
rs9378141	0.81[EUR][1000 genomes]
rs9378142	0.85[EUR][1000 genomes]
rs9380150	0.93[EUR][1000 genomes]
rs9393984	0.83[EUR][1000 genomes]
rs9393986	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9393987	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9393988	0.93[EUR][1000 genomes]
rs9393989	0.93[EUR][1000 genomes]
rs9405044	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv3332677	chr6:29733187-29961463	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3430372	chr6:29759523-29974277	Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv2758040	chr6:29792434-29975144	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv2759412	chr6:29792434-29975144	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv3391180	chr6:29798321-29977430	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	esv1848127	chr6:29817323-29966451	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv508398	chr6:29825777-30003403	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	esv3369212	chr6:29827361-29960177	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv2757159	chr6:29834472-29965501	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	esv3376588	chr6:29834667-29964324	Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
12	nsv10810	chr6:29837465-29961415	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	esv3373906	chr6:29884407-29977070	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
14	esv2641340	chr6:29913287-29978544	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	esv3378806	chr6:29913464-29978179	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
16	esv3496792	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
17	esv3496793	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
18	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
19	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
20	esv1799283	chr6:29938777-29959935	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
21	esv3444682	chr6:29952773-29957871	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4959039	HIST1H2AH	cis	cerebellum	SCAN
rs4959039	HLA-H	cis	lymphoblastoid	seeQTL
rs4959039	ZKSCAN3	cis	cerebellum	SCAN
rs4959039	HLA.A29.1	cis	multi-tissue	Pritchard
rs4959039	HLA-A	cis	lymphoblastoid	seeQTL
rs4959039	HIST1H2AI	cis	parietal	SCAN
rs4959039	BTN2A1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29945600-29966400	Weak transcription	Pancreas	Pancrea
2	chr6:29956400-29957200	Enhancers	HMEC	breast
3	chr6:29956800-29957200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:29956800-29957200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:29957000-29957400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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