Variant report

Variant	rs2961671
Chromosome Location	chr5:177620189-177620190
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11748093	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11750481	1.00[YRI][hapmap]
rs2913814	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2961663	0.81[TSI][hapmap]
rs3812071	1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]

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	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
4	nsv883190	chr5:177532201-177620189	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv1017664	chr5:177578194-177633116	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
6	nsv482872	chr5:177580298-177744381	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers 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	106 gene(s)	inside rSNPs	diseases
7	nsv883193	chr5:177591495-177620189	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv883194	chr5:177604268-177620189	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2961671	DTHD1	trans	lymphoblastoid	seeQTL
rs2961671	DHRS7	trans	lymphoblastoid	seeQTL
rs2961671	TSPAN17	cis	parietal	SCAN
rs2961671	NLGN4X	trans	lymphoblastoid	seeQTL
rs2961671	ZNF454	cis	cerebellum	SCAN
rs2961671	FAM171A1	trans	lymphoblastoid	seeQTL
rs2961671	RNF130	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177609800-177621000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:177619400-177621400	Weak transcription	Liver	Liver
3	chr5:177619600-177620800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr5:177619600-177621400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:177619800-177621800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
6	chr5:177619800-177621800	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr5:177619800-177622000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr5:177620000-177620600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:177620000-177620600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr5:177620000-177620800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:177620000-177621000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:177620000-177621000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:177620000-177621400	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr5:177620000-177621400	Enhancers	Thymus	Thymus
15	chr5:177620000-177621800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr5:177620000-177622000	Enhancers	Primary hematopoietic stem cells	blood
17	chr5:177620000-177622000	Enhancers	Fetal Thymus	thymus
18	chr5:177620000-177622600	Enhancers	Primary hematopoietic stem cells short term culture	blood

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links