Variant report

Variant	rs11079803
Chromosome Location	chr17:46019901-46019902
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	POLR2A	chr17:46018483-46020295	HepG2	liver:	n/a	n/a
2	RFX5	chr17:46018121-46020592	SK-N-SH	brain:	n/a	chr17:46018887-46018896
3	SIX5	chr17:46018362-46020053	A549	lung:	n/a	n/a
4	HEY1	chr17:46018447-46020067	HepG2	liver:	n/a	n/a
5	MYBL2	chr17:46018286-46019949	HepG2	liver:	n/a	n/a
6	POLR2A	chr17:46019724-46019907	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr17:46018386-46019976	HepG2	liver:	n/a	n/a
8	MAX	chr17:46018180-46020180	HCT-116	colon:	n/a	chr17:46019019-46019030 chr17:46019020-46019029 chr17:46019018-46019031 chr17:46019020-46019029
9	MAX	chr17:46018213-46019902	HepG2	liver:	n/a	chr17:46019019-46019030 chr17:46019020-46019029 chr17:46019018-46019031 chr17:46019020-46019029
10	MBD4	chr17:46018343-46020002	HepG2	liver:	n/a	n/a
11	SIN3AK20	chr17:46018220-46019917	MCF-7	breast:	n/a	n/a
12	POLR2A	chr17:46019747-46019913	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr17:46018533-46020053	HepG2	liver:	n/a	n/a
14	POLR2A	chr17:46018511-46019979	K562	blood:	n/a	n/a
15	POLR2A	chr17:46018333-46020145	K562	blood:	n/a	n/a
16	POLR2A	chr17:46018026-46020127	HepG2	liver:	n/a	n/a
17	ZNF263	chr17:46018571-46020154	HEK293-T-REx	kidney:	n/a	chr17:46019357-46019366 chr17:46019909-46019918 chr17:46019901-46019910
18	POLR2A	chr17:46018498-46019960	K562	blood:	n/a	n/a
19	MXI1	chr17:46017389-46019935	SK-N-SH	brain:	n/a	chr17:46019019-46019028
20	POLR2A	chr17:46018432-46020113	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:45970912..45974701-chr17:46018890..46021752,3	K562	blood:
2	chr17:46018061..46020719-chr17:46045036..46046879,2	K562	blood:
3	chr17:45915913..45917925-chr17:46018896..46020443,2	MCF-7	breast:
4	chr17:45968434..45977260-chr17:46017847..46029594,27	MCF-7	breast:
5	chr17:45915810..45917332-chr17:46018370..46020809,2	K562	blood:
6	chr17:46017765..46021634-chr17:46045854..46051133,6	MCF-7	breast:
7	chr17:45993643..45995953-chr17:46019014..46020704,3	MCF-7	breast:
8	chr17:45971510..45977679-chr17:46016123..46021422,20	MCF-7	breast:
9	chr17:46019148..46022019-chr17:46092699..46095180,2	K562	blood:
10	chr17:45978341..45980674-chr17:46019226..46022209,2	MCF-7	breast:
11	chr17:45973201..45977546-chr17:46016018..46021091,7	K562	blood:

Variant related genes	Relation type
ENSG00000234494	TF binding region
PNPO	TF binding region
ENSG00000263798	TF binding region
ENSG00000141295	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000264920	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10459927	0.82[ASN][1000 genomes]
rs11079801	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1108833	0.90[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs1130932	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11652185	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652827	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11654010	0.80[JPT][hapmap]
rs11655068	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11655352	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11659126	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11870852	0.83[ASN][1000 genomes]
rs12601827	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12602494	0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs12939739	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13353189	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs2228251	0.88[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2228253	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2229358	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2318118	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2325747	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2325749	0.81[ASN][1000 genomes]
rs2325751	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525107	0.83[ASN][1000 genomes]
rs3096	0.85[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs34593510	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35280206	0.87[ASN][1000 genomes]
rs36124074	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3764396	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4369725	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4793731	0.87[ASN][1000 genomes]
rs4793732	0.84[ASN][1000 genomes]
rs4793733	0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs4793737	0.87[ASN][1000 genomes]
rs4794261	0.83[ASN][1000 genomes]
rs4794286	0.87[ASN][1000 genomes]
rs4794332	0.87[ASN][1000 genomes]
rs6503934	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67194241	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7208707	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7211859	0.90[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs72840237	0.90[ASN][1000 genomes]
rs8066893	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8071003	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9895863	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9903223	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	nsv1062503	chr17:45977445-46021384	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS 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	22 gene(s)	inside rSNPs	diseases
5	esv1000014	chr17:46019228-46029457	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11079803	CNTNAP1	cis	parietal	SCAN
rs11079803	RP11-6N17.4	cis	Skin Sun Exposed Lower leg	GTEx
rs11079803	SP2	cis	lymphoblastoid	seeQTL
rs11079803	LRRC46	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46018200-46020000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr17:46018200-46020000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr17:46018200-46020000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
4	chr17:46018200-46020000	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr17:46018200-46020000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr17:46018200-46020000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr17:46018200-46020000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr17:46018200-46020200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:46018200-46020200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr17:46018400-46020000	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr17:46018400-46020000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr17:46018600-46020000	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr17:46018600-46020000	Active TSS	Esophagus	oesophagus
14	chr17:46018600-46020000	Active TSS	Fetal Kidney	kidney
15	chr17:46018600-46020200	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr17:46018600-46020200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr17:46018800-46020000	Active TSS	GM12878-XiMat	blood
18	chr17:46018800-46020400	Active TSS	HMEC	breast
19	chr17:46019000-46020000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr17:46019000-46020000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr17:46019200-46020000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr17:46019200-46020000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr17:46019200-46020000	Flanking Active TSS	Fetal Brain Female	brain
24	chr17:46019200-46020000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr17:46019200-46020000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
26	chr17:46019200-46020000	Flanking Active TSS	HUVEC	blood vessel
27	chr17:46019200-46020000	Flanking Active TSS	NH-A	brain
28	chr17:46019200-46020200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr17:46019200-46020200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr17:46019200-46020200	Flanking Active TSS	Fetal Thymus	thymus
31	chr17:46019200-46020200	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr17:46019400-46020000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr17:46019400-46020000	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr17:46019400-46020000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr17:46019400-46020000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr17:46019400-46020000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr17:46019400-46020000	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr17:46019400-46020000	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr17:46019400-46020000	Flanking Active TSS	Brain Substantia Nigra	brain
40	chr17:46019400-46020000	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr17:46019400-46020000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr17:46019400-46020000	Flanking Active TSS	NHLF	lung
43	chr17:46019400-46020200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr17:46019400-46020200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr17:46019400-46020200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr17:46019400-46020200	Flanking Active TSS	Dnd41	blood
47	chr17:46019400-46020200	Flanking Active TSS	Osteobl	bone
48	chr17:46019400-46020400	Flanking Active TSS	Hela-S3	cervix
49	chr17:46019600-46020000	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr17:46019600-46020000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links