Variant report

Variant	rs11768083
Chromosome Location	chr7:48134719-48134720
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:48128828..48131724-chr7:48131867..48135623,4	K562	blood:
2	chr7:48128044..48129924-chr7:48134138..48135836,2	K562	blood:
3	chr7:48134492..48136444-chr7:48138845..48140444,2	MCF-7	breast:
4	chr7:48127323..48129947-chr7:48131574..48136086,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183696	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10278152	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13227958	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13240650	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1554494	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1581415	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1581416	0.87[EUR][1000 genomes]
rs2686796	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2686800	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2686802	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2686803	0.84[EUR][1000 genomes]
rs2708866	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2708867	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2708868	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2708869	0.84[EUR][1000 genomes]
rs2708870	0.84[EUR][1000 genomes]
rs2708871	0.87[EUR][1000 genomes]
rs3752889	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3752890	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3763504	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3763505	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62447120	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6463462	0.86[GIH][hapmap]
rs6968763	0.84[EUR][1000 genomes]
rs7341420	1.00[ASW][hapmap];0.81[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7385009	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7458962	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7459020	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7793905	0.89[CEU][hapmap];0.81[CHB][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7794100	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7804178	0.93[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9639019	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9639991	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	esv997355	chr7:48128431-48138826	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11768083	UPP1	cis	cerebellum	SCAN
rs11768083	PKD1L1	cis	parietal	SCAN
rs11768083	ABCA13	cis	parietal	SCAN
rs11768083	UPP1	cis	Muscle Skeletal	GTEx
rs11768083	UPP1	cis	multi-tissue	Pritchard
rs11768083	LOC100129427	cis	cerebellum	SCAN
rs11768083	PKD1L1	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48129000-48137000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr7:48129600-48136200	Transcr. at gene 5' and 3'	NHEK	skin
3	chr7:48129600-48141000	Weak transcription	Gastric	stomach
4	chr7:48129600-48141200	Weak transcription	Ovary	ovary
5	chr7:48130000-48135600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr7:48130200-48135600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr7:48130200-48138200	Weak transcription	Pancreas	Pancrea
8	chr7:48130200-48141400	Weak transcription	Brain Substantia Nigra	brain
9	chr7:48130200-48146800	Weak transcription	Colon Smooth Muscle	Colon
10	chr7:48130200-48148200	Weak transcription	Right Atrium	heart
11	chr7:48130400-48135200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr7:48130400-48135600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr7:48130400-48135600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr7:48130400-48135600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:48130400-48135600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr7:48130400-48136000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
17	chr7:48130400-48136000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr7:48130400-48136200	Genic enhancers	Primary T cells fromperipheralblood	blood
19	chr7:48130400-48137000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr7:48130400-48141400	Weak transcription	HepG2	liver
21	chr7:48130400-48149800	Weak transcription	Fetal Kidney	kidney
22	chr7:48130400-48150000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr7:48130600-48139200	Genic enhancers	Placenta	Placenta
24	chr7:48130600-48143600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:48130800-48135600	Strong transcription	Liver	Liver
26	chr7:48130800-48149200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:48131000-48135000	Strong transcription	Left Ventricle	heart
28	chr7:48131000-48135200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr7:48131000-48135200	Strong transcription	Colonic Mucosa	Colon
30	chr7:48131000-48135200	Strong transcription	Stomach Smooth Muscle	stomach
31	chr7:48131000-48137800	Strong transcription	Fetal Intestine Small	intestine
32	chr7:48131000-48145200	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr7:48131000-48149200	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr7:48131200-48134800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr7:48131200-48135000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr7:48131200-48135200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr7:48131200-48135600	Strong transcription	Primary T cells from cord blood	blood
38	chr7:48131200-48136200	Strong transcription	Adipose Nuclei	Adipose
39	chr7:48131200-48136200	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr7:48131200-48138800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr7:48131200-48145000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr7:48131200-48148800	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr7:48131200-48149200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr7:48131400-48136400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr7:48131400-48136600	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr7:48131400-48139800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr7:48131400-48149000	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr7:48131400-48149400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr7:48131600-48134800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr7:48131600-48135200	Strong transcription	Brain Hippocampus Middle	brain

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