Variant report

Variant	rs17641524
Chromosome Location	chr1:197704717-197704718
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	FOXA1	chr1:197704448-197704803	HepG2	liver:	n/a	n/a
2	ZBTB33	chr1:197704696-197705143	K562	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZBTB41-6	chr1:197704380-197704926	NONHSAT008631

Variant related genes	Relation type
ENSG00000235582	TF binding region
DENND1B	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10737693	0.86[EUR][1000 genomes]
rs10922324	0.87[MKK][hapmap]
rs11583319	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs11588864	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12117045	0.89[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs12131588	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12134279	0.82[EUR][1000 genomes]
rs12141028	0.94[MEX][hapmap];0.85[TSI][hapmap]
rs1539414	0.94[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs16841842	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16841904	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]
rs16841912	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2224873	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2477077	0.94[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs2488389	1.00[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs2488393	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2488397	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2488398	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2488401	0.94[CEU][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6682968	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[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
rs17641524	DENND1B	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197688000-197707400	Weak transcription	Left Ventricle	heart
2	chr1:197694400-197705600	Weak transcription	Osteobl	bone
3	chr1:197694800-197707400	Weak transcription	Psoas Muscle	Psoas
4	chr1:197695800-197704800	Weak transcription	Primary B cells from cord blood	blood
5	chr1:197695800-197705400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:197695800-197705600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:197695800-197706200	Weak transcription	NHDF-Ad	bronchial
8	chr1:197695800-197708000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:197695800-197722000	Weak transcription	Fetal Lung	lung
10	chr1:197695800-197732800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:197695800-197742200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:197696000-197705600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:197696000-197705800	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr1:197696000-197706000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:197696000-197709200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr1:197696000-197716000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr1:197697000-197709000	Weak transcription	Primary T cells from cord blood	blood
18	chr1:197698200-197705200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:197698800-197708000	Weak transcription	Lung	lung
20	chr1:197699200-197707800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:197701000-197708000	Weak transcription	Small Intestine	intestine
22	chr1:197701600-197705400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:197701800-197711800	Weak transcription	Fetal Heart	heart
24	chr1:197702000-197707600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr1:197702000-197711600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:197702600-197706000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:197702600-197714200	Weak transcription	K562	blood
28	chr1:197702800-197713600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr1:197702800-197713600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr1:197702800-197743800	Weak transcription	Esophagus	oesophagus
31	chr1:197703000-197705200	Weak transcription	HMEC	breast
32	chr1:197703000-197705400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:197703000-197706000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:197703000-197709200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:197703000-197718400	Weak transcription	Dnd41	blood
36	chr1:197703400-197708000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:197704000-197706200	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:197704400-197705000	Enhancers	HepG2	liver
39	chr1:197704400-197705200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
40	chr1:197704400-197705200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:197704400-197705800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:197704400-197708000	Weak transcription	Thymus	Thymus
43	chr1:197704600-197705000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:197704600-197705000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:197704600-197705200	ZNF genes & repeats	Fetal Intestine Small	intestine
46	chr1:197704600-197706400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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