Variant report

Variant	rs1001578
Chromosome Location	chr19:42195120-42195121
allele	C/T
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	CTCF	chr19:42195090-42195782	SK-N-SH	brain:	n/a	chr19:42195489-42195502 chr19:42195333-42195346 chr19:42195487-42195505
2	BCL3	chr19:42195097-42195928	A549	lung:	n/a	n/a
3	CTCF	chr19:42195120-42195270	HAc	cerebellar:	n/a	n/a
4	CTCF	chr19:42195020-42195170	GM12873	blood:	n/a	n/a
5	CTCF	chr19:42195100-42195250	GM12867	blood:	n/a	n/a
6	CTCF	chr19:42194789-42196858	A549	lung:	n/a	chr19:42195489-42195502 chr19:42195333-42195346 chr19:42195487-42195505
7	RAD21	chr19:42194931-42195759	A549	lung:	n/a	chr19:42195489-42195499 chr19:42195485-42195504 chr19:42195488-42195501 chr19:42195487-42195499
8	CTCF	chr19:42195080-42195230	K562	blood:	n/a	n/a
9	CTCF	chr19:42195000-42195150	GM12864	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:42147995..42149203-chr19:42195085..42195974,8	MCF-7	breast:
2	chr19:42194707..42197200-chr19:42201363..42204085,2	MCF-7	breast:
3	chr19:42187020..42188703-chr19:42193918..42196262,2	K562	blood:
4	chr19:42147580..42148927-chr19:42194859..42196377,8	MCF-7	breast:
5	chr19:42148024..42148877-chr19:42195016..42195762,2	K562	blood:
6	chr19:42195068..42195942-chr19:42210669..42211245,2	MCF-7	breast:
7	chr19:42193467..42196093-chr19:42207906..42212151,3	MCF-7	breast:

Variant related genes	Relation type
CEACAM7	TF binding region
ENSG00000007306	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1001062	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10520341	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11083633	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11083635	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11671944	0.95[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11672173	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11672853	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11673394	0.82[MEX][hapmap];0.82[AMR][1000 genomes]
rs11880469	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11880615	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11880655	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12462395	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12971712	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12979028	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34652740	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3909374	0.89[EUR][1000 genomes]
rs4347734	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4802127	0.85[AMR][1000 genomes]
rs4803492	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8182595	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8182615	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8182619	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs917552	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[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	esv3319146	chr19:42082639-42212929	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv3319147	chr19:42082742-42212770	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv3422975	chr19:42106166-42212774	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	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
5	nsv1061309	chr19:42187716-42228445	Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1001578	GIPR	cis	parietal	SCAN
rs1001578	ATF5	cis	parietal	SCAN
rs1001578	PLEKHA4	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42192400-42200600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr19:42194000-42195400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:42195000-42195200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
4	chr19:42195000-42195200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr19:42195000-42195200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:42195000-42195400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:42195000-42195600	Enhancers	Pancreas	Pancrea

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