Variant report

Variant	rs7793905
Chromosome Location	chr7:48127194-48127195
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:105)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:105 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:48126896-48127267	GM12878	blood:	n/a	n/a
2	TBP	chr7:48126869-48127324	GM12878	blood:	n/a	n/a
3	CTCF	chr7:48127120-48127270	BJ	skin:	n/a	n/a
4	CHD1	chr7:48126885-48127425	GM12878	blood:	n/a	n/a
5	POLR2A	chr7:48126832-48127255	U87	brain:	n/a	n/a
6	POLR2A	chr7:48126348-48127240	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr7:48126972-48127230	MCF10A-Er-Src	breast:	n/a	n/a
8	EP300	chr7:48126936-48127313	GM12878	blood:	n/a	n/a
9	EP300	chr7:48126857-48127317	GM12878	blood:	n/a	n/a
10	CTCF	chr7:48127180-48127330	HEEpiC	esophagus:	n/a	n/a
11	TAF1	chr7:48126817-48127235	GM12878	blood:	n/a	n/a
12	CTCF	chr7:48127140-48127290	HPAF	blood vessel:	n/a	n/a
13	MAX	chr7:48126951-48127229	NB4	blood:	n/a	n/a
14	CTCF	chr7:48127140-48127290	SAEC	small airway:	n/a	n/a
15	RELA	chr7:48126954-48127401	GM19099	blood:	n/a	n/a
16	POLR2A	chr7:48126751-48129205	GM12892	blood:	n/a	n/a
17	TBL1XR1	chr7:48126994-48127326	GM12878	blood:	n/a	n/a
18	MAFK	chr7:48126537-48127236	IMR90	lung:	n/a	n/a
19	CTCF	chr7:48127120-48127270	GM12870	blood:	n/a	n/a
20	POLR2A	chr7:48126850-48129311	GM18526	blood:	n/a	n/a
21	POU2F2	chr7:48127058-48127279	GM12878	blood:	n/a	chr7:48127172-48127185
22	POLR2A	chr7:48126850-48127283	GM12878	blood:	n/a	n/a
23	CTCF	chr7:48127120-48127270	HPF	lung:	n/a	n/a
24	CTCF	chr7:48127180-48127330	HBMEC	blood vessel:	n/a	n/a
25	CTCF	chr7:48127120-48127270	HCPEpiC	choroid plexus:	n/a	n/a
26	YY1	chr7:48126986-48127396	GM12878	blood:	n/a	n/a
27	WRNIP1	chr7:48126794-48127307	GM12878	blood:	n/a	n/a
28	POU2F2	chr7:48126899-48127429	GM12878	blood:	n/a	chr7:48127172-48127185
29	CTCF	chr7:48127180-48127330	HCFaa	heart:	n/a	n/a
30	CTCF	chr7:48127100-48127250	HMF	breast:	n/a	n/a
31	BATF	chr7:48126985-48127266	GM12878	blood:	n/a	n/a
32	FOS	chr7:48126112-48127306	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr7:48126872-48129439	GM19193	blood:	n/a	n/a
34	POLR2A	chr7:48126727-48127445	U87	brain:	n/a	n/a
35	MTA3	chr7:48126690-48127427	GM12878	blood:	n/a	n/a
36	CTCF	chr7:48127060-48127210	AG09319	gingival:	n/a	n/a
37	CTCF	chr7:48127100-48127250	GM12872	blood:	n/a	n/a
38	POLR2A	chr7:48126129-48129306	GM19099	blood:	n/a	n/a
39	POLR2A	chr7:48126850-48129419	GM12892	blood:	n/a	n/a
40	CTCF	chr7:48127100-48127250	AG10803	skin:	n/a	n/a
41	POLR2A	chr7:48126894-48127283	SK-N-SH	brain:	n/a	n/a
42	CEBPB	chr7:48126403-48127348	IMR90	lung:	n/a	n/a
43	PAX5	chr7:48126910-48127505	GM12878	blood:	n/a	n/a
44	ZNF384	chr7:48127079-48127715	GM12878	blood:	n/a	n/a
45	CTCF	chr7:48127100-48127250	GM12873	blood:	n/a	n/a
46	CTCF	chr7:48127160-48127310	HBMEC	blood vessel:	n/a	n/a
47	ATF2	chr7:48126853-48127346	GM12878	blood:	n/a	n/a
48	YY1	chr7:48126975-48127396	GM12892	blood:	n/a	n/a
49	CTCF	chr7:48127080-48127230	GM12875	blood:	n/a	n/a
50	POU2F2	chr7:48126939-48127386	GM12891	blood:	n/a	chr7:48127172-48127185

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:48017456..48020295-chr7:48126750..48129913,5	K562	blood:

No data

Variant related genes	Relation type
UPP1	TF binding region
ENSG00000136273	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10278152	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11768083	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]
rs13227958	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13240650	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1554494	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1581415	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1581416	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2686796	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2686800	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2686802	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2686803	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708866	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708867	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708868	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708869	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708870	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708871	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3752889	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3752890	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3763504	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3763505	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59688958	0.86[ASN][1000 genomes]
rs62447120	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6968763	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7341420	0.81[GIH][hapmap];0.88[MEX][hapmap]
rs7458962	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7459020	0.89[CEU][hapmap];0.81[CHB][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7794100	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7804178	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9639019	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9639991	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7793905	UPP1	cis	multi-tissue	Pritchard
rs7793905	LOC100129427	cis	cerebellum	SCAN
rs7793905	PKD1L1	cis	parietal	SCAN
rs7793905	UPP1	cis	cerebellum	SCAN
rs7793905	PKD1L1	cis	cerebellum	SCAN
rs7793905	UPP1	cis	Muscle Skeletal	GTEx
rs7793905	ABCA13	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48111200-48127600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:48122000-48127800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr7:48122000-48128000	Enhancers	HMEC	breast
4	chr7:48122200-48127600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr7:48122200-48127800	Enhancers	Muscle Satellite Cultured Cells	--
6	chr7:48122200-48128000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr7:48122400-48127600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:48122400-48128000	Enhancers	NHLF	lung
9	chr7:48122400-48128200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr7:48122600-48128000	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr7:48122600-48128000	Enhancers	NHDF-Ad	bronchial
12	chr7:48122800-48128000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr7:48122800-48128000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:48123000-48127800	Enhancers	HUVEC	blood vessel
15	chr7:48123200-48127600	Weak transcription	Right Atrium	heart
16	chr7:48123200-48128000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr7:48123400-48127600	Weak transcription	Spleen	Spleen
18	chr7:48123800-48128000	Enhancers	Placenta Amnion	Placenta Amnion
19	chr7:48124000-48127600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr7:48124000-48127600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr7:48124000-48127600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr7:48124000-48127600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:48124000-48127600	Enhancers	Adipose Nuclei	Adipose
24	chr7:48124000-48127800	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr7:48124000-48127800	Enhancers	Fetal Intestine Small	intestine
26	chr7:48124000-48127800	Enhancers	Stomach Mucosa	stomach
27	chr7:48124000-48127800	Enhancers	HSMM	muscle
28	chr7:48124000-48128000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr7:48124000-48128000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr7:48124000-48128000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr7:48124000-48128000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr7:48124000-48128000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:48124000-48128000	Enhancers	Placenta	Placenta
34	chr7:48124200-48127600	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr7:48124200-48127800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr7:48124200-48127800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr7:48124200-48127800	Enhancers	Fetal Intestine Large	intestine
38	chr7:48124200-48127800	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr7:48124200-48128000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr7:48124400-48127400	Enhancers	Small Intestine	intestine
41	chr7:48124400-48127600	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr7:48124400-48127600	Enhancers	Colonic Mucosa	Colon
43	chr7:48124400-48127600	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr7:48124400-48128000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr7:48124800-48128000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr7:48125000-48127200	Enhancers	Hela-S3	cervix
47	chr7:48125000-48127600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr7:48125000-48127600	Enhancers	HepG2	liver
49	chr7:48125000-48128000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr7:48125200-48127600	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links