Variant report

Variant	rs11079812
Chromosome Location	chr17:46238276-46238277
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	GATA3	chr17:46237865-46238609	T-47D	breast:	n/a	chr17:46238583-46238604
2	TCF12	chr17:46237857-46238805	MCF-7	breast:	n/a	n/a
3	TEAD4	chr17:46237873-46238505	MCF-7	breast:	n/a	n/a
4	EP300	chr17:46237777-46238610	MCF-7	breast:	n/a	chr17:46238104-46238114 chr17:46238016-46238026 chr17:46237838-46237852 chr17:46237836-46237850
5	ZNF217	chr17:46237936-46238610	MCF-7	breast:	n/a	n/a
6	GATA3	chr17:46237739-46238797	MCF-7	breast:	n/a	chr17:46238583-46238604
7	EP300	chr17:46237976-46238402	T-47D	breast:	n/a	chr17:46238104-46238114 chr17:46238016-46238026
8	TEAD4	chr17:46237900-46238446	MCF-7	breast:	n/a	n/a
9	EP300	chr17:46237749-46238504	ECC-1	luminal epithelium:	n/a	chr17:46238104-46238114 chr17:46238016-46238026 chr17:46237838-46237852 chr17:46237836-46237850
10	GATA3	chr17:46237861-46238571	T-47D	breast:	n/a	n/a
11	FOXA1	chr17:46237851-46238563	T-47D	breast:	n/a	chr17:46238017-46238029 chr17:46238103-46238118 chr17:46238137-46238152
12	FOXA1	chr17:46237888-46238338	HepG2	liver:	n/a	chr17:46238017-46238029 chr17:46238103-46238118 chr17:46238137-46238152
13	HDAC2	chr17:46237780-46238631	MCF-7	breast:	n/a	chr17:46237835-46237849 chr17:46237840-46237854 chr17:46237834-46237848 chr17:46237837-46237851 chr17:46238615-46238629 chr17:46237839-46237853 chr17:46238611-46238625 chr17:46237836-46237850
14	SP1	chr17:46237714-46238351	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr17:46237758-46238530	MCF-7	breast:	n/a	chr17:46238076-46238086
16	FOXM1	chr17:46237715-46238544	MCF-7	breast:	n/a	n/a
17	KAP1	chr17:46237981-46238437	U2OS	brain:	n/a	chr17:46238042-46238050
18	TCF12	chr17:46237743-46238469	A549	lung:	n/a	n/a
19	NR2F2	chr17:46237781-46238548	MCF-7	breast:	n/a	n/a
20	TCF7L2	chr17:46237992-46238383	MCF-7	breast:	n/a	n/a
21	GATA3	chr17:46237707-46238706	MCF-7	breast:	n/a	chr17:46238583-46238604
22	EP300	chr17:46237848-46238592	T-47D	breast:	n/a	chr17:46238104-46238114 chr17:46238016-46238026
23	FOXA1	chr17:46237900-46238406	ECC-1	luminal epithelium:	n/a	chr17:46238017-46238029 chr17:46238103-46238118 chr17:46238137-46238152
24	FOXA1	chr17:46237798-46238531	T-47D	breast:	n/a	chr17:46238017-46238029 chr17:46238103-46238118 chr17:46238137-46238152
25	SIN3AK20	chr17:46237677-46238705	MCF-7	breast:	n/a	n/a
26	TCF12	chr17:46237839-46238367	H1-hESC	embryonic stem cell:	n/a	n/a
27	FOXM1	chr17:46237846-46238496	MCF-7	breast:	n/a	n/a
28	SIN3AK20	chr17:46237656-46238787	MCF-7	breast:	n/a	n/a
29	FOXA1	chr17:46237898-46238320	HepG2	liver:	n/a	chr17:46238017-46238029 chr17:46238103-46238118 chr17:46238137-46238152
30	GATA3	chr17:46237902-46238481	MCF-7	breast:	n/a	n/a
31	NR2F2	chr17:46237710-46238616	MCF-7	breast:	n/a	n/a
32	FOXA1	chr17:46237928-46238287	HepG2	liver:	n/a	chr17:46238017-46238029 chr17:46238103-46238118 chr17:46238137-46238152
33	HDAC2	chr17:46237846-46238323	H1-hESC	embryonic stem cell:	n/a	n/a
34	TCF12	chr17:46237743-46238614	MCF-7	breast:	n/a	n/a
35	FOXA2	chr17:46237907-46238510	A549	lung:	n/a	chr17:46238017-46238029
36	CTCF	chr17:46238140-46238290	A549	lung:	n/a	n/a
37	CEBPB	chr17:46237895-46238461	MCF-7	breast:	n/a	chr17:46238195-46238212
38	FOXA1	chr17:46237926-46238296	HepG2	liver:	n/a	chr17:46238017-46238029 chr17:46238103-46238118 chr17:46238137-46238152
39	TCF12	chr17:46237787-46238470	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr17:46238197-46238411	ProgFib	skin:	n/a	n/a
41	MAX	chr17:46237856-46238439	MCF-7	breast:	n/a	chr17:46238076-46238086
42	EP300	chr17:46237881-46238484	MCF-7	breast:	n/a	chr17:46238104-46238114 chr17:46238016-46238026
43	FOXA1	chr17:46237934-46238296	ECC-1	luminal epithelium:	n/a	chr17:46238017-46238029 chr17:46238103-46238118 chr17:46238137-46238152
44	ELF1	chr17:46237849-46238423	MCF-7	breast:	n/a	n/a
45	FOXA2	chr17:46237883-46238501	A549	lung:	n/a	chr17:46238017-46238029
46	TCF12	chr17:46237883-46238430	ECC-1	luminal epithelium:	n/a	n/a
47	HDAC2	chr17:46237857-46238587	MCF-7	breast:	n/a	n/a
48	ZEB1	chr17:46237817-46238332	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46236677..46239400-chr17:46239909..46241915,2	K562	blood:
2	chr17:46237804..46239741-chr17:46316113..46318637,2	MCF-7	breast:
3	chr17:46102851..46105314-chr17:46237154..46238995,2	MCF-7	breast:

Variant related genes	Relation type
MIR1203	TF binding region
ENSG00000141293	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11079811	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11868509	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs12449324	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12449529	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12601412	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12602010	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12948653	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12953085	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1316643	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16954750	0.81[YRI][hapmap]
rs17619103	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2525103	0.84[CEU][hapmap]
rs34130316	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34449497	0.89[ASN][1000 genomes]
rs35371915	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35999311	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7215582	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7221416	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7224648	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11079812	KRT13	cis	parietal	SCAN
rs11079812	PNPO	cis	cerebellum	SCAN
rs11079812	PNPO	cis	parietal	SCAN
rs11079812	NAGLU	cis	parietal	SCAN
rs11079812	RPRML	cis	parietal	SCAN
rs11079812	ASB16	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46216400-46251400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr17:46220800-46249000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr17:46221600-46238400	Weak transcription	Fetal Thymus	thymus
4	chr17:46230600-46245000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr17:46231000-46243800	Weak transcription	Primary B cells from cord blood	blood
6	chr17:46232000-46239000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr17:46232000-46239800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr17:46234000-46240600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr17:46234400-46238400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr17:46234400-46239600	Weak transcription	GM12878-XiMat	blood
11	chr17:46234400-46240600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr17:46235600-46240600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr17:46236000-46241200	Enhancers	Fetal Intestine Large	intestine
14	chr17:46236000-46250200	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr17:46236200-46244200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr17:46236400-46240600	Enhancers	Fetal Kidney	kidney
17	chr17:46236400-46241200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr17:46236400-46241200	Enhancers	Fetal Intestine Small	intestine
19	chr17:46236400-46242600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr17:46236600-46239200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr17:46236600-46239200	Strong transcription	Primary B cells from peripheral blood	blood
22	chr17:46236600-46239400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
23	chr17:46236600-46242600	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr17:46236800-46240000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
25	chr17:46236800-46244200	Strong transcription	Primary T cells from cord blood	blood
26	chr17:46237000-46240400	Enhancers	Duodenum Mucosa	Duodenum
27	chr17:46237000-46241200	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr17:46237200-46239800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr17:46237200-46240800	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr17:46237400-46242000	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr17:46237600-46238400	Enhancers	Small Intestine	intestine
32	chr17:46237600-46238400	Enhancers	A549	lung
33	chr17:46237600-46239200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr17:46237800-46238400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr17:46237800-46238800	Flanking Active TSS	Liver	Liver
36	chr17:46237800-46239800	Enhancers	HepG2	liver
37	chr17:46238000-46238400	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr17:46238000-46238400	Enhancers	Pancreas	Pancrea
39	chr17:46238000-46238600	Strong transcription	Thymus	Thymus
40	chr17:46238000-46240800	Weak transcription	Gastric	stomach
41	chr17:46238200-46238400	Flanking Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr17:46238200-46238400	Flanking Active TSS	H9 Cell Line	embryonic stem cell
43	chr17:46238200-46238600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr17:46238200-46238600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr17:46238200-46238600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr17:46238200-46238600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr17:46238200-46238600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
48	chr17:46238200-46238600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
49	chr17:46238200-46240000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr17:46238200-46240200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood

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