Variant report

Variant	rs1992561
Chromosome Location	chr17:20219119-20219120
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10491107	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204300	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204423	0.87[EUR][1000 genomes]
rs11653630	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11653869	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11654942	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11657161	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11658116	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11868116	0.84[EUR][1000 genomes]
rs11869258	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12453013	0.89[EUR][1000 genomes]
rs12603372	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12936443	0.84[EUR][1000 genomes]
rs12938355	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12942568	0.91[EUR][1000 genomes]
rs12942627	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12949481	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12950564	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1373146	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960697	0.84[EUR][1000 genomes]
rs1859407	0.86[EUR][1000 genomes]
rs1974745	0.84[EUR][1000 genomes]
rs2013443	0.84[EUR][1000 genomes]
rs2042046	0.84[EUR][1000 genomes]
rs2107565	0.87[EUR][1000 genomes]
rs2158472	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2189709	0.86[EUR][1000 genomes]
rs2526459	0.86[EUR][1000 genomes]
rs2526463	0.86[EUR][1000 genomes]
rs2526465	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2526466	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2526476	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2526477	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2526478	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2526481	0.92[EUR][1000 genomes]
rs2526482	0.91[EUR][1000 genomes]
rs2526486	0.88[EUR][1000 genomes]
rs2703770	0.91[EUR][1000 genomes]
rs2703771	0.93[EUR][1000 genomes]
rs2703776	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2703777	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2703781	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2703786	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2703788	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2703795	0.86[EUR][1000 genomes]
rs2703800	0.87[EUR][1000 genomes]
rs2703803	0.89[EUR][1000 genomes]
rs2703805	0.90[EUR][1000 genomes]
rs2703807	0.90[EUR][1000 genomes]
rs2703812	0.90[EUR][1000 genomes]
rs2703814	0.91[EUR][1000 genomes]
rs2703819	0.92[EUR][1000 genomes]
rs3850779	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3850780	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925086	0.84[EUR][1000 genomes]
rs4925087	0.84[EUR][1000 genomes]
rs4925090	0.86[EUR][1000 genomes]
rs4925091	0.86[EUR][1000 genomes]
rs55705283	0.84[EUR][1000 genomes]
rs57837691	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62066865	0.81[EUR][1000 genomes]
rs62066870	0.86[EUR][1000 genomes]
rs6587219	0.84[EUR][1000 genomes]
rs67217337	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7212500	0.83[EUR][1000 genomes]
rs7212571	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7216599	0.83[EUR][1000 genomes]
rs7216794	0.83[EUR][1000 genomes]
rs7219615	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7219908	0.83[EUR][1000 genomes]
rs7222984	0.83[EUR][1000 genomes]
rs7222987	0.84[EUR][1000 genomes]
rs7223476	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73309111	0.95[ASN][1000 genomes]
rs733794	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs757494	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs757495	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8066143	0.83[EUR][1000 genomes]
rs8071274	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8078716	0.83[EUR][1000 genomes]
rs8080649	0.86[EUR][1000 genomes]
rs9893832	0.83[EUR][1000 genomes]
rs9898080	0.84[EUR][1000 genomes]
rs9901336	0.86[EUR][1000 genomes]
rs9901796	0.85[EUR][1000 genomes]
rs9902032	0.83[EUR][1000 genomes]
rs9907516	0.84[EUR][1000 genomes]
rs9912844	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067100	chr17:20007480-20464520	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv543260	chr17:20007480-20464520	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv428669	chr17:20071969-20245033	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1064854	chr17:20086562-20225751	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv2761953	chr17:20086562-20225763	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv574581	chr17:20088492-20699545	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
7	nsv1065758	chr17:20141912-20464366	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv543262	chr17:20141912-20464366	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	nsv1057389	chr17:20158343-20256498	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv427993	chr17:20171398-20482061	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	nsv916440	chr17:20171468-20839266	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
12	nsv520772	chr17:20184501-20522444	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
13	nsv521025	chr17:20198024-20514921	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1992561	SPECC1	Cis_1M	lymphoblastoid	RTeQTL
rs1992561	KRT16P3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20187800-20223800	Weak transcription	Pancreas	Pancrea
2	chr17:20201000-20220000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr17:20210800-20223800	Weak transcription	Colonic Mucosa	Colon
4	chr17:20210800-20223800	Weak transcription	Esophagus	oesophagus
5	chr17:20211000-20219600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr17:20211000-20223000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr17:20211000-20223800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr17:20211000-20223800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:20211000-20224000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr17:20211000-20224000	Weak transcription	HMEC	breast
11	chr17:20211200-20221600	Weak transcription	Small Intestine	intestine
12	chr17:20211200-20223800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr17:20211200-20224000	Weak transcription	Fetal Intestine Large	intestine
14	chr17:20211400-20220800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr17:20211400-20224000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr17:20211600-20221800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr17:20211600-20224000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr17:20212200-20222000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr17:20212400-20219800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr17:20213000-20222000	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr17:20213000-20223800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr17:20213000-20223800	Weak transcription	Adipose Nuclei	Adipose
23	chr17:20213000-20226600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr17:20213200-20223800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr17:20214400-20223400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr17:20214600-20220200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr17:20216000-20219600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr17:20216200-20219400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr17:20216600-20219200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr17:20216600-20219200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr17:20216600-20219400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr17:20216600-20219400	Strong transcription	Aorta	Aorta
33	chr17:20216600-20219400	Strong transcription	Hela-S3	cervix
34	chr17:20216600-20221400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr17:20216800-20219400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr17:20217000-20219400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr17:20217000-20219600	Strong transcription	Osteobl	bone
38	chr17:20217200-20219200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr17:20217200-20219600	Genic enhancers	Brain Hippocampus Middle	brain
40	chr17:20217200-20224000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr17:20217400-20219200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr17:20217600-20219200	Strong transcription	Ovary	ovary
43	chr17:20217800-20221200	Weak transcription	Fetal Brain Female	brain
44	chr17:20218000-20219400	Strong transcription	Fetal Intestine Small	intestine
45	chr17:20218000-20220200	Weak transcription	Lung	lung
46	chr17:20218000-20221000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr17:20218000-20221400	Weak transcription	Fetal Stomach	stomach
48	chr17:20218200-20219400	Genic enhancers	Brain Angular Gyrus	brain
49	chr17:20218400-20219400	Enhancers	Brain Cingulate Gyrus	brain
50	chr17:20218400-20219600	Enhancers	Brain Substantia Nigra	brain

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