Variant report

Variant	rs1952151
Chromosome Location	chr14:21540863-21540864
allele	G/T
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	SMC3	chr14:21536425-21540907	SK-N-SH	brain:	n/a	chr14:21536769-21536783
2	MAZ	chr14:21536460-21541162	IMR90	lung:	n/a	chr14:21536927-21536936 chr14:21539487-21539497 chr14:21538216-21538226 chr14:21539744-21539754
3	ZNF263	chr14:21538413-21541547	HEK293-T-REx	kidney:	n/a	chr14:21539767-21539776 chr14:21539753-21539774 chr14:21540466-21540475 chr14:21540463-21540472
4	POLR2A	chr14:21536635-21541667	IMR90	lung:	n/a	n/a
5	CHD1	chr14:21536437-21541448	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:21537028..21541987-chr14:21553672..21557659,5	MCF-7	breast:
2	chr14:21539183..21541334-chr14:21547839..21549455,2	K562	blood:
3	chr14:21535299..21541334-chr14:21568487..21576770,16	MCF-7	breast:
4	chr14:21535130..21541812-chr14:21564802..21576767,22	MCF-7	breast:
5	chr14:21538435..21540879-chr14:21565246..21568452,4	K562	blood:
6	chr14:21539634..21541782-chr14:21548249..21551082,2	MCF-7	breast:
7	chr14:21540755..21543423-chr14:21560916..21563307,2	K562	blood:
8	chr14:21534879..21542621-chr14:21563384..21568050,9	MCF-7	breast:

Variant related genes	Relation type
NDRG2	TF binding region
ARHGEF40	TF binding region
ENSG00000165801	Chromatin interaction
ENSG00000165804	Chromatin interaction
ENSG00000232070	Chromatin interaction
ENSG00000178107	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11629332	0.87[ASN][1000 genomes]
rs1243472	0.86[ASN][1000 genomes]
rs1958395	0.89[ASN][1000 genomes]
rs3827911	0.87[CHB][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs3827913	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4982404	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4982405	0.86[ASN][1000 genomes]
rs4982406	0.83[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs7140850	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7143633	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs7149011	0.82[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs8019890	0.95[GIH][hapmap];0.82[TSI][hapmap]
rs943991	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	nsv832740	chr14:21332060-21545052	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS 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	45 gene(s)	inside rSNPs	diseases
2	nsv530009	chr14:21377022-22044608	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
3	nsv530769	chr14:21407536-22139126	Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	nsv916319	chr14:21507092-21896590	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	nsv1036762	chr14:21507093-22101805	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv541976	chr14:21507093-22101805	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
7	nsv826882	chr14:21511021-21604201	Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv530770	chr14:21526410-21852363	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
9	nsv528337	chr14:21540863-21565189	Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv525724	chr14:21540863-21574690	Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1952151	LRP10	cis	cerebellum	SCAN
rs1952151	ANG	cis	cerebellum	SCAN
rs1952151	OR4K14	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:21538800-21541000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr14:21539000-21541200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr14:21539600-21541000	Enhancers	Spleen	Spleen
4	chr14:21539800-21543200	Weak transcription	Esophagus	oesophagus
5	chr14:21540000-21541000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr14:21540000-21541000	Enhancers	Brain Substantia Nigra	brain
7	chr14:21540000-21541000	Weak transcription	Lung	lung
8	chr14:21540000-21541200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
9	chr14:21540000-21541200	Enhancers	Hela-S3	cervix
10	chr14:21540200-21541000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr14:21540200-21541000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr14:21540200-21541000	Enhancers	Primary B cells from peripheral blood	blood
13	chr14:21540200-21541000	Genic enhancers	HepG2	liver
14	chr14:21540200-21541200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr14:21540200-21541200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr14:21540200-21541200	Weak transcription	Aorta	Aorta
17	chr14:21540200-21541200	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr14:21540200-21541200	Enhancers	Placenta	Placenta
19	chr14:21540200-21541200	Bivalent Enhancer	Fetal Thymus	thymus
20	chr14:21540200-21541200	Weak transcription	Left Ventricle	heart
21	chr14:21540200-21541400	Enhancers	Liver	Liver
22	chr14:21540200-21541800	Enhancers	Stomach Mucosa	stomach
23	chr14:21540200-21542200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr14:21540200-21544000	Weak transcription	Psoas Muscle	Psoas
25	chr14:21540400-21541000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr14:21540400-21541000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr14:21540400-21541000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr14:21540400-21541000	Enhancers	Primary hematopoietic stem cells	blood
29	chr14:21540400-21541000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr14:21540400-21541000	Weak transcription	Right Ventricle	heart
31	chr14:21540400-21541000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr14:21540400-21541000	Flanking Active TSS	NHDF-Ad	bronchial
33	chr14:21540400-21541200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr14:21540400-21541200	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr14:21540400-21541200	Enhancers	Brain Cingulate Gyrus	brain
36	chr14:21540400-21541200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr14:21540400-21541200	Enhancers	Colonic Mucosa	Colon
38	chr14:21540400-21541200	Enhancers	Duodenum Mucosa	Duodenum
39	chr14:21540400-21541200	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr14:21540400-21541400	Enhancers	Brain Anterior Caudate	brain
41	chr14:21540400-21541400	Enhancers	Brain Hippocampus Middle	brain
42	chr14:21540400-21541400	Genic enhancers	Rectal Smooth Muscle	rectum
43	chr14:21540400-21542400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr14:21540400-21542400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
45	chr14:21540400-21543200	Genic enhancers	Fetal Muscle Leg	muscle
46	chr14:21540400-21543400	Weak transcription	Brain Angular Gyrus	brain
47	chr14:21540400-21547000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr14:21540600-21541000	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr14:21540600-21541000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr14:21540600-21541000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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