Variant report

Variant	rs2878404
Chromosome Location	chr16:72045186-72045187
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:72042919..72045492-chr16:72049478..72051025,2	K562	blood:
2	chr16:72042016..72045516-chr16:72126835..72130601,4	K562	blood:
3	chr16:72042306..72048206-chr16:72125753..72130155,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140829	Chromatin interaction
ENSG00000140830	Chromatin interaction
ENSG00000102967	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10048144	0.92[ASN][1000 genomes]
rs1465457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288002	0.81[CHD][hapmap]
rs2550868	0.83[CHD][hapmap]
rs3764310	0.94[ASW][hapmap];0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4788454	0.92[GIH][hapmap];0.89[JPT][hapmap]
rs4788456	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4788597	0.92[CEU][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4788598	0.92[CEU][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4788600	0.88[CEU][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs752434	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8048262	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8062895	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs929866	0.92[GIH][hapmap];0.89[JPT][hapmap]
rs9932951	0.81[CHD][hapmap]

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	nsv1056439	chr16:71916498-72051144	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1055854	chr16:71922144-72082886	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv833273	chr16:71971805-72152854	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	nsv906894	chr16:72013539-72046211	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	n/a
9	esv1843253	chr16:72042428-72059149	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2878404	DHODH	cis	cerebellum	SCAN
rs2878404	HP	cis	multi-tissue	Pritchard
rs2878404	VPS4A	cis	cerebellum	SCAN
rs2878404	FBXL8	cis	parietal	SCAN
rs2878404	CCDC79	cis	parietal	SCAN
rs2878404	DHODH	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72043000-72046000	Weak transcription	Spleen	Spleen
2	chr16:72043000-72046800	Weak transcription	Fetal Heart	heart
3	chr16:72043000-72049600	Weak transcription	Aorta	Aorta
4	chr16:72043000-72063000	Weak transcription	Small Intestine	intestine
5	chr16:72043200-72045200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr16:72043200-72045600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr16:72043200-72045600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr16:72043200-72045600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr16:72043200-72045600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr16:72043200-72045600	Weak transcription	Fetal Muscle Leg	muscle
11	chr16:72043200-72045800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr16:72043200-72045800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr16:72043200-72045800	Weak transcription	Fetal Intestine Small	intestine
14	chr16:72043200-72045800	Weak transcription	Fetal Stomach	stomach
15	chr16:72043200-72046000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr16:72043200-72046000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr16:72043200-72046000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr16:72043200-72046000	Weak transcription	Fetal Intestine Large	intestine
19	chr16:72043200-72046000	Weak transcription	Right Atrium	heart
20	chr16:72043200-72046000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr16:72043200-72046200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr16:72043200-72046200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr16:72043200-72046200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr16:72043200-72046200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr16:72043200-72046400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr16:72043200-72046400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr16:72043200-72046400	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr16:72043200-72046400	Weak transcription	Brain Anterior Caudate	brain
29	chr16:72043200-72046400	Weak transcription	Brain Germinal Matrix	brain
30	chr16:72043200-72046400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr16:72043200-72046400	Weak transcription	Esophagus	oesophagus
32	chr16:72043200-72046400	Weak transcription	Fetal Brain Female	brain
33	chr16:72043200-72046400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr16:72043200-72046400	Weak transcription	NHEK	skin
35	chr16:72043200-72046400	Weak transcription	NHLF	lung
36	chr16:72043200-72046600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr16:72043200-72046600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr16:72043200-72046600	Weak transcription	Left Ventricle	heart
39	chr16:72043200-72046800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr16:72043200-72046800	Weak transcription	Right Ventricle	heart
41	chr16:72043200-72047000	Weak transcription	Placenta	Placenta
42	chr16:72043200-72047000	Weak transcription	Ovary	ovary
43	chr16:72043200-72047000	Weak transcription	Stomach Mucosa	stomach
44	chr16:72043200-72047200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr16:72043200-72047200	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr16:72043200-72047200	Weak transcription	Adipose Nuclei	Adipose
47	chr16:72043200-72047200	Weak transcription	Brain Hippocampus Middle	brain
48	chr16:72043200-72047200	Weak transcription	Lung	lung
49	chr16:72043200-72047200	Weak transcription	Psoas Muscle	Psoas
50	chr16:72043200-72047200	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links