Variant report

Variant	rs16841904
Chromosome Location	chr1:197701992-197701993
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	FOXA2	chr1:197701978-197702883	HepG2	liver:	n/a	chr1:197702247-197702259

No.	Distal block	Cell Line	Cell type
1	chr1:197697770..197700203-chr1:197701390..197704214,2	K562	blood:
2	chr1:197701490..197704107-chr1:197709565..197711301,2	K562	blood:
3	chr1:197620433..197622127-chr1:197700140..197702120,2	K562	blood:
4	chr1:197686076..197688310-chr1:197699419..197702157,2	K562	blood:

Variant related genes	Relation type
ENSG00000235582	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10737693	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11583319	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.86[ASN][1000 genomes]
rs11588864	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11799915	0.91[ASN][1000 genomes]
rs12092948	0.98[ASN][1000 genomes]
rs12117045	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12131588	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12134279	0.81[EUR][1000 genomes]
rs12141028	1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.86[ASN][1000 genomes]
rs12354257	1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1421399	0.87[ASN][1000 genomes]
rs1539414	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1573100	1.00[ASN][1000 genomes]
rs16841842	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16841912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17564924	0.91[ASN][1000 genomes]
rs17641524	1.00[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1775448	0.93[ASN][1000 genomes]
rs1775452	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1998598	0.89[ASN][1000 genomes]
rs2224873	0.84[EUR][1000 genomes]
rs2477059	1.00[ASN][1000 genomes]
rs2477073	0.93[ASN][1000 genomes]
rs2477077	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2488389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2488391	0.90[ASN][1000 genomes]
rs2488393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2488397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488401	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2884629	0.86[ASN][1000 genomes]
rs35939830	0.86[ASN][1000 genomes]
rs4316387	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6682968	0.85[EUR][1000 genomes]
rs6702421	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873075	chr1:197464448-197714851	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv437263	chr1:197599030-197722240	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv427908	chr1:197611569-197767362	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16841904	DENND1B	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197688000-197707400	Weak transcription	Left Ventricle	heart
2	chr1:197692800-197702600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:197694400-197705600	Weak transcription	Osteobl	bone
4	chr1:197694800-197707400	Weak transcription	Psoas Muscle	Psoas
5	chr1:197695800-197702600	Weak transcription	Liver	Liver
6	chr1:197695800-197704600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:197695800-197704600	Weak transcription	Fetal Intestine Small	intestine
8	chr1:197695800-197704800	Weak transcription	Primary B cells from cord blood	blood
9	chr1:197695800-197705400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:197695800-197705600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:197695800-197706200	Weak transcription	NHDF-Ad	bronchial
12	chr1:197695800-197708000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:197695800-197722000	Weak transcription	Fetal Lung	lung
14	chr1:197695800-197732800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:197695800-197742200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr1:197696000-197702400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:197696000-197702800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:197696000-197705600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:197696000-197705800	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr1:197696000-197706000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:197696000-197709200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:197696000-197716000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:197697000-197709000	Weak transcription	Primary T cells from cord blood	blood
24	chr1:197698200-197705200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:197698800-197708000	Weak transcription	Lung	lung
26	chr1:197699200-197707800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:197700800-197702800	Strong transcription	Primary hematopoietic stem cells	blood
28	chr1:197700800-197703000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:197701000-197703000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:197701000-197708000	Weak transcription	Small Intestine	intestine
31	chr1:197701200-197703000	Strong transcription	Dnd41	blood
32	chr1:197701400-197702000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:197701400-197702600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:197701400-197702600	Enhancers	K562	blood
35	chr1:197701400-197702800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr1:197701600-197702200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:197701600-197705400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:197701800-197702600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:197701800-197702800	Enhancers	Brain Anterior Caudate	brain
40	chr1:197701800-197703400	Enhancers	HepG2	liver
41	chr1:197701800-197711800	Weak transcription	Fetal Heart	heart

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