Variant report

Variant	rs625978
Chromosome Location	chr11:67344664-67344665
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:67339423..67342315-chr11:67342794..67345312,3	K562	blood:
2	chr11:67339423..67341248-chr11:67342794..67345312,3	K562	blood:
3	chr11:67342273..67345213-chr11:67395722..67399867,4	K562	blood:
4	chr11:67344270..67346942-chr11:67379351..67381800,2	MCF-7	breast:
5	chr11:67343943..67344868-chr11:67373946..67374859,3	MCF-7	breast:
6	chr11:67343427..67347334-chr11:67376017..67380328,4	K562	blood:
7	chr11:67344360..67352769-chr11:67395394..67400721,12	K562	blood:
8	chr11:67309805..67311983-chr11:67342547..67345264,2	K562	blood:
9	chr11:67342278..67344841-chr11:67347504..67351094,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000184224	Chromatin interaction
ENSG00000084207	Chromatin interaction
ENSG00000231793	Chromatin interaction
ENSG00000167799	Chromatin interaction
ENSG00000167792	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10896179	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10896180	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10896186	0.88[CHB][hapmap]
rs11227837	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12225376	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1254123	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1262166	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1269981	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1531514	0.84[CHB][hapmap]
rs2008922	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2276118	0.89[CHB][hapmap]
rs2370141	0.80[CEU][hapmap]
rs2508459	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3765088	0.88[CHB][hapmap]
rs4147581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs591434	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs598811	0.81[ASN][1000 genomes]
rs611663	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs614080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638140	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs640777	0.89[ASN][1000 genomes]
rs645653	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs656652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs658768	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6591256	0.82[CEU][hapmap]
rs666328	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs674783	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684928	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs694746	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7106423	0.82[CEU][hapmap]
rs762803	0.80[CEU][hapmap]
rs7941395	0.82[CEU][hapmap]
rs7941648	0.82[CEU][hapmap]
rs7952081	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1043037	chr11:67027193-67357425	Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv897801	chr11:67033076-67432479	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
4	nsv897807	chr11:67155210-67414492	Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
5	nsv897808	chr11:67155210-67419855	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
6	nsv534229	chr11:67164667-67411909	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
7	esv2422195	chr11:67234322-67626901	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Weak transcription 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 miRNA target site	146 gene(s)	inside rSNPs	diseases
8	nsv1041988	chr11:67319916-67749246	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
9	nsv897814	chr11:67339949-67460529	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv1050463	chr11:67343421-67717338	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs625978	NUDT8	cis	Heart Left Ventricle	GTEx
rs625978	PTPRCAP	cis	Nerve Tibial	GTEx
rs625978	RPS6KB2	cis	multi-tissue	Pritchard
rs625978	DOC2GP	cis	Skin Sun Exposed Lower leg	GTEx
rs625978	PTPRCAP	cis	Heart Left Ventricle	GTEx
rs625978	PTPRCAP	cis	Thyroid	GTEx
rs625978	RPS6KB2	cis	Lymphoblastoid	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67336400-67345200	Weak transcription	Gastric	stomach
2	chr11:67340600-67346800	Weak transcription	Pancreas	Pancrea
3	chr11:67340800-67344800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:67340800-67346600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr11:67341200-67345600	Weak transcription	HepG2	liver
6	chr11:67341400-67346000	Weak transcription	Fetal Intestine Large	intestine
7	chr11:67341400-67346600	Weak transcription	A549	lung
8	chr11:67342600-67345600	Weak transcription	Fetal Intestine Small	intestine
9	chr11:67342600-67347000	Weak transcription	Hela-S3	cervix
10	chr11:67343800-67346600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr11:67344200-67345000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr11:67344400-67344800	Enhancers	Right Ventricle	heart
13	chr11:67344400-67345000	Enhancers	H1 Cell Line	embryonic stem cell
14	chr11:67344400-67346000	Enhancers	Placenta	Placenta
15	chr11:67344400-67350600	Enhancers	Stomach Mucosa	stomach
16	chr11:67344600-67344800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr11:67344600-67345200	Enhancers	K562	blood

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