Variant report

Variant	rs2023929
Chromosome Location	chr16:72236956-72236957
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72231856..72234002-chr16:72234236..72237028,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10492815	1.00[ASW][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap]
rs12051317	1.00[ASW][hapmap]
rs16970667	0.94[ASN][1000 genomes]
rs217181	0.84[CHD][hapmap]
rs3852789	0.95[ASN][1000 genomes]
rs61483465	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	esv2758430	chr16:71976344-72274347	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	esv2758654	chr16:71976344-72274347	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv428329	chr16:71976344-72274347	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
6	nsv534588	chr16:72078262-72287230	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
8	nsv1059599	chr16:72219769-72342170	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1066473	chr16:72229094-72373598	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2023929	DHODH	cis	cerebellum	SCAN
rs2023929	E2F4	cis	parietal	SCAN
rs2023929	CCDC79	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72229200-72240200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr16:72232400-72237000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr16:72233000-72237200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr16:72233000-72240400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr16:72233200-72240000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr16:72233800-72237000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr16:72234000-72237000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr16:72234200-72237600	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr16:72235000-72237000	Weak transcription	Brain Anterior Caudate	brain
10	chr16:72235400-72238000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr16:72235400-72238000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr16:72235800-72237800	Enhancers	Duodenum Mucosa	Duodenum
13	chr16:72235800-72237800	Enhancers	Fetal Intestine Large	intestine
14	chr16:72235800-72238000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr16:72235800-72238000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr16:72235800-72238000	Enhancers	Fetal Intestine Small	intestine
17	chr16:72235800-72238000	Enhancers	HMEC	breast
18	chr16:72236000-72237400	Enhancers	NHDF-Ad	bronchial
19	chr16:72236000-72237600	Enhancers	Pancreas	Pancrea
20	chr16:72236000-72238000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr16:72236000-72240800	Weak transcription	Fetal Brain Male	brain
22	chr16:72236200-72237000	Enhancers	Fetal Brain Female	brain
23	chr16:72236200-72237200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr16:72236200-72238000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr16:72236200-72238000	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr16:72236400-72237000	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr16:72236400-72237800	Enhancers	Fetal Lung	lung
28	chr16:72236400-72238000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr16:72236400-72238000	Enhancers	Stomach Mucosa	stomach
30	chr16:72236400-72238400	Enhancers	Primary B cells from peripheral blood	blood
31	chr16:72236600-72237000	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr16:72236600-72237000	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr16:72236600-72237000	Flanking Active TSS	NHEK	skin
34	chr16:72236600-72237200	Enhancers	Muscle Satellite Cultured Cells	--
35	chr16:72236600-72237200	Enhancers	HUVEC	blood vessel
36	chr16:72236600-72237400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr16:72236600-72237400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr16:72236600-72237800	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr16:72236600-72237800	Enhancers	Brain Hippocampus Middle	brain
40	chr16:72236600-72238000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr16:72236600-72238000	Enhancers	Esophagus	oesophagus
42	chr16:72236600-72244000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr16:72236800-72237000	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr16:72236800-72237000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr16:72236800-72237000	Enhancers	GM12878-XiMat	blood
46	chr16:72236800-72237200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr16:72236800-72237200	Enhancers	HepG2	liver
48	chr16:72236800-72237600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr16:72236800-72237800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr16:72236800-72238000	Enhancers	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links