Variant report

Variant	rs11878239
Chromosome Location	chr19:42257156-42257157
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	SPI1	chr19:42257049-42257461	HL-60	blood:	n/a	n/a
2	CTCF	chr19:42257100-42257250	HFF-Myc	foreskin:	n/a	n/a
3	CTCF	chr19:42257076-42257415	H1-hESC	embryonic stem cell:	n/a	chr19:42257276-42257294 chr19:42257278-42257299 chr19:42257279-42257292 chr19:42257279-42257288 chr19:42257281-42257291 chr19:42257279-42257292 chr19:42257277-42257293
4	CTCF	chr19:42257149-42257404	GM10266	blood:	n/a	chr19:42257276-42257294 chr19:42257278-42257299 chr19:42257279-42257292 chr19:42257279-42257288 chr19:42257281-42257291 chr19:42257279-42257292 chr19:42257277-42257293
5	CTCF	chr19:42256965-42257595	K562	blood:	n/a	chr19:42257276-42257294 chr19:42257278-42257299 chr19:42257279-42257292 chr19:42257279-42257288 chr19:42257281-42257291 chr19:42257279-42257292 chr19:42257277-42257293
6	SPI1	chr19:42257086-42257340	GM12891	blood:	n/a	n/a
7	RAD21	chr19:42257147-42257376	K562	blood:	n/a	chr19:42257282-42257292 chr19:42257280-42257293 chr19:42257277-42257296
8	RAD21	chr19:42257112-42257533	H1-hESC	embryonic stem cell:	n/a	chr19:42257282-42257292 chr19:42257280-42257293 chr19:42257277-42257296
9	CTCF	chr19:42257120-42257270	AG04450	lung:	n/a	n/a
10	CTCF	chr19:42257052-42257438	K562	blood:	n/a	chr19:42257276-42257294 chr19:42257278-42257299 chr19:42257279-42257292 chr19:42257279-42257288 chr19:42257281-42257291 chr19:42257279-42257292 chr19:42257277-42257293
11	RUNX3	chr19:42257104-42257449	GM12878	blood:	n/a	n/a
12	CTCF	chr19:42257146-42257413	GM19238	blood:	n/a	chr19:42257276-42257294 chr19:42257278-42257299 chr19:42257279-42257292 chr19:42257279-42257288 chr19:42257281-42257291 chr19:42257279-42257292 chr19:42257277-42257293
13	CTCF	chr19:42255195-42260167	A549	lung:	n/a	chr19:42257276-42257294 chr19:42257278-42257299 chr19:42257279-42257292 chr19:42257279-42257288 chr19:42257281-42257291 chr19:42257279-42257292 chr19:42257277-42257293
14	CTCF	chr19:42256884-42257570	SK-N-SH	brain:	n/a	chr19:42257276-42257294 chr19:42257278-42257299 chr19:42257279-42257292 chr19:42257279-42257288 chr19:42257281-42257291 chr19:42257279-42257292 chr19:42257277-42257293
15	CTCF	chr19:42257143-42257412	Gliobla	brain:	n/a	chr19:42257276-42257294 chr19:42257278-42257299 chr19:42257279-42257292 chr19:42257279-42257288 chr19:42257281-42257291 chr19:42257279-42257292 chr19:42257277-42257293
16	RAD21	chr19:42257127-42257362	GM12878	blood:	n/a	chr19:42257282-42257292 chr19:42257280-42257293 chr19:42257277-42257296
17	CTCF	chr19:42257140-42257290	GM12864	blood:	n/a	chr19:42257279-42257288
18	CTCF	chr19:42257120-42257270	WI-38	lung:	n/a	n/a
19	RAD21	chr19:42257050-42257445	MCF-7	breast:	n/a	chr19:42257282-42257292 chr19:42257280-42257293 chr19:42257277-42257296
20	RAD21	chr19:42257012-42257505	HCT-116	colon:	n/a	chr19:42257282-42257292 chr19:42257280-42257293 chr19:42257277-42257296
21	CTCF	chr19:42257111-42257456	IMR90	lung:	n/a	chr19:42257276-42257294 chr19:42257278-42257299 chr19:42257279-42257292 chr19:42257279-42257288 chr19:42257281-42257291 chr19:42257279-42257292 chr19:42257277-42257293
22	SMC3	chr19:42257107-42257446	K562	blood:	n/a	chr19:42257278-42257292 chr19:42257282-42257292
23	CTCF	chr19:42257044-42257458	HepG2	liver:	n/a	chr19:42257276-42257294 chr19:42257278-42257299 chr19:42257279-42257292 chr19:42257279-42257288 chr19:42257281-42257291 chr19:42257279-42257292 chr19:42257277-42257293
24	CTCF	chr19:42257064-42257442	H1-hESC	embryonic stem cell:	n/a	chr19:42257276-42257294 chr19:42257278-42257299 chr19:42257279-42257292 chr19:42257279-42257288 chr19:42257281-42257291 chr19:42257279-42257292 chr19:42257277-42257293
25	CTCF	chr19:42257040-42257442	MCF-7	breast:	n/a	chr19:42257276-42257294 chr19:42257278-42257299 chr19:42257279-42257292 chr19:42257279-42257288 chr19:42257281-42257291 chr19:42257279-42257292 chr19:42257277-42257293
26	RAD21	chr19:42257040-42257437	MCF-7	breast:	n/a	chr19:42257282-42257292 chr19:42257280-42257293 chr19:42257277-42257296
27	CTCF	chr19:42257140-42257290	NHDF-neo	bronchial:	n/a	chr19:42257279-42257288
28	MAZ	chr19:42257129-42257357	K562	blood:	n/a	n/a
29	CTCF	chr19:42257114-42257401	ECC-1	luminal epithelium:	n/a	chr19:42257276-42257294 chr19:42257278-42257299 chr19:42257279-42257292 chr19:42257279-42257288 chr19:42257281-42257291 chr19:42257279-42257292 chr19:42257277-42257293
30	CTCF	chr19:42257080-42257230	HAc	cerebellar:	n/a	n/a
31	CTCF	chr19:42257056-42257493	T-47D	breast:	n/a	chr19:42257276-42257294 chr19:42257278-42257299 chr19:42257279-42257292 chr19:42257279-42257288 chr19:42257281-42257291 chr19:42257279-42257292 chr19:42257277-42257293
32	CTCF	chr19:42257118-42257397	HUVEC	blood vessel:	n/a	chr19:42257276-42257294 chr19:42257278-42257299 chr19:42257279-42257292 chr19:42257279-42257288 chr19:42257281-42257291 chr19:42257279-42257292 chr19:42257277-42257293
33	CTCF	chr19:42257044-42257442	HCT-116	colon:	n/a	chr19:42257276-42257294 chr19:42257278-42257299 chr19:42257279-42257292 chr19:42257279-42257288 chr19:42257281-42257291 chr19:42257279-42257292 chr19:42257277-42257293
34	CTCF	chr19:42257124-42257386	GM10248	blood:	n/a	chr19:42257276-42257294 chr19:42257278-42257299 chr19:42257279-42257292 chr19:42257279-42257288 chr19:42257281-42257291 chr19:42257279-42257292 chr19:42257277-42257293
35	CTCF	chr19:42257140-42257290	GM12801	blood:	n/a	chr19:42257279-42257288
36	YY1	chr19:42257117-42257354	GM12878	blood:	n/a	chr19:42257269-42257283 chr19:42257201-42257217
37	RAD21	chr19:42257147-42257407	H1-hESC	embryonic stem cell:	n/a	chr19:42257282-42257292 chr19:42257280-42257293 chr19:42257277-42257296
38	RAD21	chr19:42256962-42257508	A549	lung:	n/a	chr19:42257282-42257292 chr19:42257280-42257293 chr19:42257277-42257296
39	CTCF	chr19:42257100-42257250	HA-sp	spinal cord:	n/a	n/a
40	CTCF	chr19:42257137-42257407	Medullo	brain:	n/a	chr19:42257276-42257294 chr19:42257278-42257299 chr19:42257279-42257292 chr19:42257279-42257288 chr19:42257281-42257291 chr19:42257279-42257292 chr19:42257277-42257293
41	CTCF	chr19:42257137-42257414	K562	blood:	n/a	chr19:42257276-42257294 chr19:42257278-42257299 chr19:42257279-42257292 chr19:42257279-42257288 chr19:42257281-42257291 chr19:42257279-42257292 chr19:42257277-42257293
42	CTCF	chr19:42257132-42257396	HepG2	liver:	n/a	chr19:42257276-42257294 chr19:42257278-42257299 chr19:42257279-42257292 chr19:42257279-42257288 chr19:42257281-42257291 chr19:42257279-42257292 chr19:42257277-42257293
43	CTCF	chr19:42257140-42257290	HCT-116	colon:	n/a	chr19:42257279-42257288
44	ELF1	chr19:42257134-42257407	GM12878	blood:	n/a	n/a
45	RAD21	chr19:42256995-42257459	HCT-116	colon:	n/a	chr19:42257282-42257292 chr19:42257280-42257293 chr19:42257277-42257296
46	CTCF	chr19:42256997-42257429	Spleen_OC	spleen:	n/a	chr19:42257276-42257294 chr19:42257278-42257299 chr19:42257279-42257292 chr19:42257279-42257288 chr19:42257281-42257291 chr19:42257279-42257292 chr19:42257277-42257293
47	CTCF	chr19:42257121-42257398	SK-N-SH_RA	brain:	n/a	chr19:42257276-42257294 chr19:42257278-42257299 chr19:42257279-42257292 chr19:42257279-42257288 chr19:42257281-42257291 chr19:42257279-42257292 chr19:42257277-42257293
48	RUNX3	chr19:42257095-42257434	GM12878	blood:	n/a	n/a
49	CTCF	chr19:42257140-42257290	HFF	foreskin:	n/a	chr19:42257279-42257288
50	ZNF143	chr19:42257152-42257388	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:42256878..42257460-chr19:42288323..42288994,2	MCF-7	breast:
2	chr19:42214835..42216861-chr19:42256777..42258757,2	MCF-7	breast:
3	chr19:42210733..42211670-chr19:42256878..42258361,4	K562	blood:
4	chr19:42256872..42257731-chr19:42277925..42278830,2	MCF-7	breast:
5	chr19:42254797..42261680-chr19:42284783..42292674,12	MCF-7	breast:
6	chr19:42256268..42257789-chr19:42259874..42261531,2	MCF-7	breast:
7	chr19:42256816..42257733-chr19:42462027..42462557,2	K562	blood:
8	chr19:42255651..42257648-chr19:42288124..42290756,2	MCF-7	breast:
9	chr19:42256322..42257851-chr19:42324890..42325806,7	K562	blood:
10	chr19:42256392..42258478-chr19:42289082..42290564,19	MCF-7	breast:

Variant related genes	Relation type
CEACAM6	TF binding region
ENSG00000268833	Chromatin interaction
ENSG00000007306	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10403308	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10406899	0.82[ASN][1000 genomes]
rs10408799	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10411488	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10412553	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10414063	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10415317	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10415946	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10417322	0.82[ASN][1000 genomes]
rs10421687	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10425443	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10853754	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11083637	0.80[ASN][1000 genomes]
rs1115885	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11667651	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11672324	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11673394	0.83[CHB][hapmap]
rs11878262	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11881921	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12971712	0.83[CHB][hapmap]
rs12973096	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12985771	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1593086	0.82[ASN][1000 genomes]
rs2002926	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2113133	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2113134	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2161625	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3764577	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3764579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3829668	0.94[CHB][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3928916	0.83[CHB][hapmap]
rs4239514	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4802128	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4802129	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802130	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803503	0.82[ASN][1000 genomes]
rs4803505	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803506	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55997514	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7252828	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7255070	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs748249	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8106723	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs987066	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	esv3425986	chr19:42212540-42259719	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv579615	chr19:42221434-42310388	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv3430577	chr19:42247653-42285973	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv911774	chr19:42250325-42288821	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv3384883	chr19:42253458-42288853	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv3319044	chr19:42257039-42297123	Bivalent Enhancer Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv3319045	chr19:42257039-42297123	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11878239	DBP	cis	parietal	SCAN
rs11878239	SLC1A5	cis	parietal	SCAN
rs11878239	SIGLEC11	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42254400-42260200	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr19:42254600-42258000	Enhancers	Stomach Mucosa	stomach
3	chr19:42254800-42259200	Weak transcription	Fetal Intestine Small	intestine
4	chr19:42255200-42259000	Weak transcription	Colonic Mucosa	Colon
5	chr19:42255400-42257600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:42255400-42259200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr19:42255800-42259000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr19:42256400-42258400	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr19:42256600-42257200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr19:42256800-42257800	Weak transcription	Pancreas	Pancrea
11	chr19:42257000-42258200	Weak transcription	Colon Smooth Muscle	Colon
12	chr19:42257000-42259200	Weak transcription	Esophagus	oesophagus

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