Variant report

Variant	rs16841842
Chromosome Location	chr1:197611682-197611683
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:197610998..197613034-chr1:197615077..197617017,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10737693	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11583319	0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11588864	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11799915	0.98[ASN][1000 genomes]
rs12092948	0.96[ASN][1000 genomes]
rs12117045	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12118913	0.87[AMR][1000 genomes]
rs12131588	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12141028	0.84[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12354257	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[ASN][1000 genomes]
rs12724239	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12748009	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1421399	0.93[ASN][1000 genomes]
rs1539414	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs1573100	0.93[ASN][1000 genomes]
rs16841904	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];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];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17564924	0.98[ASN][1000 genomes]
rs17621130	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17641524	1.00[CEU][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1775448	1.00[ASN][1000 genomes]
rs1775452	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1998598	0.87[ASN][1000 genomes]
rs2224873	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2477059	0.93[ASN][1000 genomes]
rs2477073	1.00[ASN][1000 genomes]
rs2477077	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2488389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488391	0.84[ASN][1000 genomes]
rs2488393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2488397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2488398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2488401	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2884629	0.92[ASN][1000 genomes]
rs35939830	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4316387	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6682968	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6702421	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873074	chr1:197464448-197698103	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	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
3	nsv548872	chr1:197529218-197644581	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv873076	chr1:197529218-197689967	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	esv3397065	chr1:197545083-197637033	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	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
7	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
rs16841842	DENND1B	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197542000-197626400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:197553000-197629800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:197590000-197613400	Weak transcription	Stomach Mucosa	stomach
4	chr1:197593600-197628400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:197596600-197644800	Weak transcription	Ovary	ovary
6	chr1:197598800-197628600	Weak transcription	NHDF-Ad	bronchial
7	chr1:197599200-197628600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:197602800-197615200	Weak transcription	Pancreas	Pancrea
9	chr1:197602800-197625000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr1:197602800-197641400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr1:197603000-197612600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:197603000-197614000	Weak transcription	Lung	lung
13	chr1:197603000-197620400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr1:197603000-197621200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:197603000-197625200	Weak transcription	Thymus	Thymus
16	chr1:197603000-197627800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:197603000-197628600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:197603000-197632400	Weak transcription	Fetal Lung	lung
19	chr1:197603000-197632600	Weak transcription	Small Intestine	intestine
20	chr1:197603200-197625000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:197603200-197625200	Weak transcription	Left Ventricle	heart
22	chr1:197603200-197626600	Weak transcription	Fetal Stomach	stomach
23	chr1:197603200-197628400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:197603200-197645000	Weak transcription	Esophagus	oesophagus
25	chr1:197603400-197618000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:197603400-197624800	Weak transcription	Right Ventricle	heart
27	chr1:197603400-197643400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:197604000-197626400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:197604000-197628200	Weak transcription	Liver	Liver
30	chr1:197604200-197635200	Weak transcription	Aorta	Aorta
31	chr1:197604600-197626400	Weak transcription	Primary T cells from cord blood	blood
32	chr1:197604800-197611800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:197605400-197612200	Strong transcription	Dnd41	blood
34	chr1:197607800-197622800	Weak transcription	NH-A	brain
35	chr1:197608400-197615200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:197608400-197628400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr1:197608600-197631400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:197608800-197612800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:197609000-197613800	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr1:197609000-197614000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:197609000-197628000	Weak transcription	Fetal Kidney	kidney
42	chr1:197609600-197611800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr1:197609600-197613800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:197609600-197621600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr1:197609800-197613200	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr1:197609800-197614400	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:197610000-197612800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:197610200-197612600	Weak transcription	Brain Substantia Nigra	brain
49	chr1:197610200-197626200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:197610200-197640000	Weak transcription	Fetal Intestine Small	intestine

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