Variant report

Variant	rs402098
Chromosome Location	chr1:242363698-242363699
allele	C/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	MYC	chr1:242362920-242364357	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr1:242363449-242364252	MCF10A-Er-Src	breast:	n/a	chr1:242363574-242363582
3	STAT3	chr1:242363350-242364056	MCF10A-Er-Src	breast:	n/a	chr1:242363574-242363582
4	STAT3	chr1:242363338-242363776	MCF10A-Er-Src	breast:	n/a	chr1:242363574-242363582
5	POLR2A	chr1:242363440-242363753	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr1:242363233-242364101	MCF10A-Er-Src	breast:	n/a	n/a
7	MYC	chr1:242363074-242364024	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr1:242363266-242364410	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr1:242363235-242363893	MCF10A-Er-Src	breast:	n/a	n/a
10	SETDB1	chr1:242363053-242364124	U2OS	brain:	n/a	n/a
11	STAT3	chr1:242363455-242364061	MCF10A-Er-Src	breast:	n/a	chr1:242363574-242363582

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:242363202..242365570-chr1:242368002..242370016,2	K562	blood:
2	chr1:242353836..242355949-chr1:242363634..242366630,2	K562	blood:

Variant related genes	Relation type
ENSG00000224525	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs172738	1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs178428	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2636251	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653165	0.97[ASN][1000 genomes]
rs2840621	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs316823	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs316825	0.97[ASN][1000 genomes]
rs316828	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs316829	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs316833	0.81[EUR][1000 genomes]
rs316834	0.81[EUR][1000 genomes]
rs316837	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs316854	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316856	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316858	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316859	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316860	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316861	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316862	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316865	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316866	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316867	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420622	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs427498	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6429339	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv948409	chr1:241830086-242489705	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv468672	chr1:242201247-242555949	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv470788	chr1:242201247-242555949	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv549462	chr1:242201247-242555949	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv528016	chr1:242223399-242451350	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv549463	chr1:242265419-242856854	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv998804	chr1:242281003-242491362	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv430391	chr1:242307104-243280885	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv817488	chr1:242330066-243121127	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv868888	chr1:242330066-243191101	Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv1003844	chr1:242363698-242904755	Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs402098	PLD5	cis	cerebellum	SCAN
rs402098	WDR64	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:242353200-242366200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:242353400-242380400	Weak transcription	Aorta	Aorta
3	chr1:242359400-242364200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:242360600-242366200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr1:242361200-242364600	Enhancers	HMEC	breast
6	chr1:242361600-242365000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:242361800-242369200	Weak transcription	Adipose Nuclei	Adipose
8	chr1:242362200-242366400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:242362600-242364800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:242362800-242363800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
11	chr1:242362800-242364000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:242362800-242364800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
13	chr1:242363000-242364400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:242363000-242364400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:242363000-242364400	Enhancers	NHEK	skin
16	chr1:242363000-242371400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:242363400-242363800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:242363400-242364400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:242363400-242364600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:242363600-242364000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links