Variant report

Variant	rs40985
Chromosome Location	chr5:16841992-16841993
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10213765	0.86[ASN][1000 genomes]
rs10213824	0.83[ASN][1000 genomes]
rs13164534	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13181529	0.87[ASN][1000 genomes]
rs13187027	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs173786	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs17651266	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17651344	0.88[CEU][hapmap];0.86[ASN][1000 genomes]
rs17707735	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17707780	0.86[ASN][1000 genomes]
rs185235	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs253333	0.90[ASN][1000 genomes]
rs2560861	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs31499	0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs34029608	0.83[ASN][1000 genomes]
rs34055160	0.88[ASN][1000 genomes]
rs35145816	0.86[ASN][1000 genomes]
rs62369354	0.93[ASN][1000 genomes]
rs62370982	0.86[ASN][1000 genomes]
rs62370983	0.86[ASN][1000 genomes]
rs716555	0.83[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.92[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	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv3529928	chr5:16748426-16856563	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
3	esv3529929	chr5:16748426-16856563	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv1030550	chr5:16748966-16872084	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	esv2762500	chr5:16815489-16952565	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv461987	chr5:16834568-16848200	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv597310	chr5:16834568-16848200	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16818000-16846600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:16820200-16842600	Weak transcription	HMEC	breast
3	chr5:16820400-16845400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr5:16820600-16845000	Weak transcription	NH-A	brain
5	chr5:16820800-16843000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:16820800-16855200	Weak transcription	HSMM	muscle
7	chr5:16825400-16842800	Weak transcription	NHLF	lung
8	chr5:16828000-16852400	Weak transcription	NHDF-Ad	bronchial
9	chr5:16828400-16842800	Weak transcription	NHEK	skin
10	chr5:16829400-16842400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:16829400-16855800	Weak transcription	Fetal Intestine Small	intestine
12	chr5:16830000-16842400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:16830400-16846600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:16832400-16855000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:16834400-16846200	Weak transcription	Osteobl	bone
16	chr5:16834600-16842400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:16834600-16842400	Weak transcription	Gastric	stomach
18	chr5:16834800-16853400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr5:16836400-16843400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr5:16838200-16853600	Weak transcription	Fetal Muscle Leg	muscle
21	chr5:16839000-16853000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:16839000-16855800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:16839000-16864600	Weak transcription	Fetal Brain Female	brain
24	chr5:16839200-16849600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:16839600-16842200	Weak transcription	Fetal Brain Male	brain
26	chr5:16840600-16842400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:16840600-16842400	Weak transcription	Lung	lung
28	chr5:16840600-16843200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:16841200-16842000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:16841200-16842000	Enhancers	Brain Substantia Nigra	brain
31	chr5:16841200-16843200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:16841200-16843800	Enhancers	Fetal Lung	lung
33	chr5:16841400-16842000	Genic enhancers	A549	lung
34	chr5:16841400-16842400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:16841400-16842400	Enhancers	Stomach Mucosa	stomach
36	chr5:16841400-16842600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:16841600-16842000	Enhancers	Adipose Nuclei	Adipose
38	chr5:16841600-16842000	Flanking Active TSS	Ovary	ovary
39	chr5:16841600-16842400	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr5:16841600-16842600	Enhancers	HUVEC	blood vessel
41	chr5:16841600-16842800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr5:16841600-16843600	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr5:16841600-16843600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:16841600-16843600	Enhancers	Fetal Kidney	kidney
45	chr5:16841800-16842600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr5:16841800-16842800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr5:16841800-16843400	Enhancers	Pancreas	Pancrea
48	chr5:16841800-16843600	Enhancers	HSMMtube	muscle
49	chr5:16841800-16843800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr5:16841800-16852400	Weak transcription	Fetal Stomach	stomach

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