Variant report

Variant	rs6463462
Chromosome Location	chr7:48142194-48142195
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	POLR2A	chr7:48141485-48142543	U87	brain:	n/a	n/a
2	POLR2A	chr7:48140716-48143588	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr7:48141459-48142659	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr7:48140899-48143448	A549	lung:	n/a	n/a
5	CTCF	chr7:48142060-48142210	GM12866	blood:	n/a	n/a
6	POLR2A	chr7:48141660-48143203	HCT-116	colon:	n/a	n/a
7	CTCF	chr7:48142180-48142330	HMEC	breast:	n/a	n/a
8	CTCF	chr7:48142100-48142250	WERI-Rb-1	eye:	n/a	n/a
9	POLR2A	chr7:48141479-48143568	U87	brain:	n/a	n/a
10	POLR2A	chr7:48142152-48142714	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:48140103..48142604-chr7:48146519..48148132,2	K562	blood:
2	chr7:48139477..48142399-chr7:48149802..48152490,2	K562	blood:

Variant related genes	Relation type
UPP1	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11768083	0.86[GIH][hapmap]
rs13228276	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7341420	0.88[CEU][hapmap];0.89[CHB][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7385009	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7459020	0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1027414	chr7:48117684-48438543	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6463462	PKD1L1	cis	parietal	SCAN
rs6463462	UPP1	cis	Muscle Skeletal	GTEx
rs6463462	PKD1L1	cis	cerebellum	SCAN
rs6463462	UPP1	cis	cerebellum	SCAN
rs6463462	LOC100129427	cis	cerebellum	SCAN
rs6463462	ABCA13	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48130200-48146800	Weak transcription	Colon Smooth Muscle	Colon
2	chr7:48130200-48148200	Weak transcription	Right Atrium	heart
3	chr7:48130400-48149800	Weak transcription	Fetal Kidney	kidney
4	chr7:48130400-48150000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr7:48130600-48143600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr7:48130800-48149200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:48131000-48145200	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr7:48131000-48149200	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr7:48131200-48145000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:48131200-48148800	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr7:48131200-48149200	Strong transcription	Duodenum Mucosa	Duodenum
12	chr7:48131400-48149000	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr7:48131400-48149400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr7:48131600-48142200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:48131600-48148800	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr7:48131600-48149000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr7:48131600-48149600	Weak transcription	Thymus	Thymus
18	chr7:48132200-48146400	Weak transcription	Small Intestine	intestine
19	chr7:48132200-48149200	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr7:48134200-48149600	Weak transcription	GM12878-XiMat	blood
21	chr7:48134400-48148000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr7:48135200-48149000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr7:48135200-48149400	Strong transcription	A549	lung
24	chr7:48136200-48144800	Weak transcription	Fetal Stomach	stomach
25	chr7:48137200-48144800	Strong transcription	Osteobl	bone
26	chr7:48137200-48149400	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr7:48137600-48143600	Strong transcription	NH-A	brain
28	chr7:48137600-48149200	Strong transcription	HMEC	breast
29	chr7:48137600-48150200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr7:48137800-48149000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr7:48137800-48149000	Strong transcription	Lung	lung
32	chr7:48137800-48149200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr7:48137800-48149200	Strong transcription	NHEK	skin
34	chr7:48137800-48149600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr7:48137800-48152400	Weak transcription	HSMM	muscle
36	chr7:48138000-48142600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
37	chr7:48138000-48149800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr7:48138200-48142600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr7:48138200-48148800	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr7:48138400-48148800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr7:48138400-48149200	Strong transcription	Esophagus	oesophagus
42	chr7:48138400-48149800	Weak transcription	Primary B cells from cord blood	blood
43	chr7:48138600-48145000	Strong transcription	Right Ventricle	heart
44	chr7:48138600-48148600	Strong transcription	HUVEC	blood vessel
45	chr7:48138600-48149000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr7:48138800-48149200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr7:48138800-48149800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr7:48138800-48156200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:48139000-48142400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr7:48139200-48148600	Strong transcription	Placenta	Placenta

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