Variant report

Variant	rs4799327
Chromosome Location	chr18:29674992-29674993
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	FAM48A	chr18:29674912-29675074	GM12878	blood:	n/a	n/a
2	POLR2A	chr18:29671561-29677909	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29671668..29674127-chr18:29674569..29677601,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000265008	TF binding region
ENSG00000134758	Chromatin interaction
ENSG00000265008	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs16962699	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[ASN][1000 genomes]
rs16962701	0.93[ASW][hapmap];0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17735362	1.00[JPT][hapmap]
rs4239374	1.00[CHB][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs4799328	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4799630	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55786778	0.86[ASN][1000 genomes]
rs56273402	0.82[ASN][1000 genomes]
rs56360277	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56810557	0.84[ASN][1000 genomes]
rs61271315	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67074695	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs68037424	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7229437	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7230167	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[ASN][1000 genomes]
rs7234604	1.00[CHB][hapmap]
rs7237971	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73415858	0.86[ASN][1000 genomes]
rs73415859	0.84[ASN][1000 genomes]
rs73415860	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757673	chr18:29632749-29674992	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2758719	chr18:29632749-29674992	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv909522	chr18:29645496-29674992	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv909523	chr18:29645496-29679922	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1055457	chr18:29654978-29677371	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4799327	DSC1	cis	cerebellum	SCAN
rs4799327	RNF138	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29671200-29675000	Active TSS	GM12878-XiMat	blood
2	chr18:29672600-29676000	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr18:29673400-29675000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
4	chr18:29673400-29692800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr18:29673400-29713800	Weak transcription	Spleen	Spleen
6	chr18:29673600-29675400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr18:29673600-29675400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr18:29673600-29678400	Flanking Active TSS	Primary T cells from cord blood	blood
9	chr18:29673800-29675200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr18:29673800-29675200	Enhancers	Adipose Nuclei	Adipose
11	chr18:29673800-29675200	Enhancers	Brain Hippocampus Middle	brain
12	chr18:29673800-29675800	Weak transcription	Left Ventricle	heart
13	chr18:29673800-29675800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr18:29673800-29676400	Weak transcription	Aorta	Aorta
15	chr18:29673800-29676400	Enhancers	Brain Angular Gyrus	brain
16	chr18:29673800-29676600	Enhancers	Brain Cingulate Gyrus	brain
17	chr18:29673800-29676600	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr18:29673800-29676600	Enhancers	Brain Substantia Nigra	brain
19	chr18:29673800-29676800	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr18:29673800-29677000	Enhancers	Fetal Heart	heart
21	chr18:29673800-29678000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr18:29673800-29679400	Weak transcription	Gastric	stomach
23	chr18:29673800-29702000	Weak transcription	Pancreas	Pancrea
24	chr18:29673800-29714000	Weak transcription	Esophagus	oesophagus
25	chr18:29673800-29714200	Weak transcription	Ovary	ovary
26	chr18:29673800-29715200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr18:29673800-29715200	Weak transcription	Lung	lung
28	chr18:29673800-29715800	Weak transcription	Colonic Mucosa	Colon
29	chr18:29673800-29717000	Weak transcription	HSMMtube	muscle
30	chr18:29674000-29675000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr18:29674000-29675200	Enhancers	Fetal Intestine Small	intestine
32	chr18:29674000-29675400	Enhancers	Stomach Mucosa	stomach
33	chr18:29674000-29676000	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr18:29674000-29676000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr18:29674000-29676400	Genic enhancers	Primary B cells from peripheral blood	blood
36	chr18:29674000-29677400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr18:29674000-29679000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr18:29674000-29679600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr18:29674000-29689200	Weak transcription	Right Atrium	heart
40	chr18:29674000-29692600	Weak transcription	Placenta	Placenta
41	chr18:29674000-29712000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr18:29674200-29675200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr18:29674200-29675200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr18:29674200-29675400	Transcr. at gene 5' and 3'	K562	blood
45	chr18:29674200-29676400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr18:29674200-29676400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr18:29674200-29677800	Genic enhancers	Primary monocytes fromperipheralblood	blood
48	chr18:29674200-29692800	Weak transcription	HSMM	muscle
49	chr18:29674200-29693000	Weak transcription	Fetal Muscle Trunk	muscle
50	chr18:29674400-29675000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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