Variant report

Variant	rs4780057
Chromosome Location	chr15:33178499-33178500
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:33177002..33179276-chr15:33196689..33199398,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11072039	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12050712	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12050715	0.92[EUR][1000 genomes]
rs2339162	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3110560	0.92[EUR][1000 genomes]
rs347932	0.85[EUR][1000 genomes]
rs347933	0.85[EUR][1000 genomes]
rs347936	0.92[EUR][1000 genomes]
rs347937	0.82[TSI][hapmap];0.91[EUR][1000 genomes]
rs347940	1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs347941	0.92[EUR][1000 genomes]
rs347942	1.00[MEX][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs347943	0.92[EUR][1000 genomes]
rs347946	0.90[EUR][1000 genomes]
rs477827	0.92[EUR][1000 genomes]
rs4779595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4779596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4780055	0.83[MEX][hapmap]
rs481087	0.84[CEU][hapmap];0.90[EUR][1000 genomes]
rs481430	1.00[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs494584	0.90[EUR][1000 genomes]
rs509083	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs512644	0.90[EUR][1000 genomes]
rs512752	0.90[EUR][1000 genomes]
rs536558	0.88[EUR][1000 genomes]
rs536612	0.88[EUR][1000 genomes]
rs538535	0.88[EUR][1000 genomes]
rs567682	0.90[EUR][1000 genomes]
rs579064	0.89[EUR][1000 genomes]
rs580115	0.90[EUR][1000 genomes]
rs62001320	0.90[EUR][1000 genomes]
rs62001355	0.91[EUR][1000 genomes]
rs62001356	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs692950	1.00[MEX][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs7162186	1.00[ASW][hapmap];0.94[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7165928	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7170830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8027463	0.83[MEX][hapmap]
rs8030196	0.91[EUR][1000 genomes]
rs8030367	0.91[EUR][1000 genomes]
rs8030557	0.92[EUR][1000 genomes]
rs8031188	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422296	chr15:32798938-33221215	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv456785	chr15:32926076-33352989	Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv568913	chr15:32926076-33352989	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv832962	chr15:33111517-33239736	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv903978	chr15:33144202-33308641	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv1041609	chr15:33148035-33355999	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv542339	chr15:33148035-33355999	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv903980	chr15:33149087-33264201	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv568917	chr15:33167171-33304172	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4780057	TJP1	cis	cerebellum	SCAN
rs4780057	SCG5	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33138800-33190600	Weak transcription	Thymus	Thymus
2	chr15:33139600-33190600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr15:33147000-33191400	Weak transcription	Lung	lung
4	chr15:33149000-33202000	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr15:33154400-33192800	Weak transcription	Colonic Mucosa	Colon
6	chr15:33154400-33216800	Weak transcription	Fetal Thymus	thymus
7	chr15:33155000-33208200	Weak transcription	Fetal Kidney	kidney
8	chr15:33160000-33201800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:33162200-33202400	Weak transcription	Gastric	stomach
10	chr15:33165600-33178600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:33166000-33202400	Weak transcription	Pancreas	Pancrea
12	chr15:33166200-33211800	Weak transcription	HSMMtube	muscle
13	chr15:33170600-33186800	Weak transcription	Spleen	Spleen
14	chr15:33170800-33196200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr15:33170800-33200400	Weak transcription	NH-A	brain
16	chr15:33171800-33180200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:33171800-33180600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr15:33172000-33181600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr15:33172400-33179000	Weak transcription	Aorta	Aorta
20	chr15:33174000-33182000	Enhancers	Colon Smooth Muscle	Colon
21	chr15:33174000-33182000	Enhancers	Rectal Smooth Muscle	rectum
22	chr15:33175400-33178600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr15:33175600-33185000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr15:33176400-33179000	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr15:33176400-33179600	Enhancers	Fetal Stomach	stomach
26	chr15:33177000-33178800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:33177000-33180200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr15:33177200-33178800	Strong transcription	Osteobl	bone
29	chr15:33177200-33180400	Weak transcription	NHLF	lung
30	chr15:33177600-33178800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr15:33177600-33179800	Weak transcription	HSMM	muscle
32	chr15:33178000-33179400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr15:33178000-33190800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr15:33178200-33179200	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr15:33178200-33180200	Weak transcription	NHDF-Ad	bronchial
36	chr15:33178200-33180600	Strong transcription	Placenta	Placenta
37	chr15:33178400-33179000	Enhancers	H1 Cell Line	embryonic stem cell
38	chr15:33178400-33179000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr15:33178400-33179200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:33178400-33179200	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr15:33178400-33179200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:33178400-33179200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr15:33178400-33179400	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr15:33178400-33179600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:33178400-33180800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr15:33178400-33190400	Weak transcription	Monocytes-CD14+_RO01746	blood

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