Variant report

Variant	rs203469
Chromosome Location	chr17:19806404-19806405
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11204419	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11204420	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs119672	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1479129	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1638525	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs166840	0.87[EUR][1000 genomes]
rs169412	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs169414	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs175921	0.84[ASN][1000 genomes]
rs175922	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs191865	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs203450	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203451	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203452	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203455	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs203456	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203457	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203458	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203459	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs203460	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203461	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203462	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203465	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203466	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203470	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs203477	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203479	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203481	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203482	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2108978	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs397969	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs427798	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4925060	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56153261	0.88[ASN][1000 genomes]
rs6587206	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7222403	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8066150	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs850623	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs860335	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9899357	0.81[EUR][1000 genomes]
rs9907752	0.82[ASN][1000 genomes]
rs9914273	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9914304	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv482398	chr17:19673458-19808039	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS 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 miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs203469	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19796400-19809800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:19799200-19808400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:19799800-19806800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr17:19799800-19807000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr17:19800600-19807600	Weak transcription	Brain Angular Gyrus	brain
6	chr17:19801000-19808200	Weak transcription	Left Ventricle	heart
7	chr17:19801000-19808400	Weak transcription	Esophagus	oesophagus
8	chr17:19801400-19806600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr17:19801400-19806800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr17:19801400-19808200	Weak transcription	Right Ventricle	heart
11	chr17:19801400-19808400	Weak transcription	Fetal Kidney	kidney
12	chr17:19801400-19808400	Weak transcription	Gastric	stomach
13	chr17:19801400-19808400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr17:19801400-19808600	Weak transcription	Colonic Mucosa	Colon
15	chr17:19801400-19808600	Weak transcription	Small Intestine	intestine
16	chr17:19801400-19809000	Weak transcription	Psoas Muscle	Psoas
17	chr17:19801400-19814200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr17:19801600-19808400	Weak transcription	Brain Anterior Caudate	brain
19	chr17:19801600-19808400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr17:19801600-19808800	Weak transcription	Fetal Heart	heart
21	chr17:19801600-19808800	Weak transcription	K562	blood
22	chr17:19801600-19814600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr17:19802000-19806800	Weak transcription	NH-A	brain
24	chr17:19802000-19808400	Weak transcription	NHEK	skin
25	chr17:19802200-19806600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr17:19802200-19806800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr17:19802200-19807400	Weak transcription	HUVEC	blood vessel
28	chr17:19802200-19809000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr17:19802200-19814200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr17:19802600-19806800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr17:19802600-19806800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr17:19802800-19807600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr17:19802800-19824000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr17:19802800-19829000	Strong transcription	Fetal Muscle Leg	muscle
35	chr17:19802800-19844400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr17:19802800-19846400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr17:19802800-19852400	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr17:19803000-19806800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr17:19803000-19807000	Strong transcription	Fetal Stomach	stomach
40	chr17:19803000-19807400	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr17:19803000-19807400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr17:19803000-19810400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr17:19803000-19810400	Strong transcription	Stomach Smooth Muscle	stomach
44	chr17:19803000-19813200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr17:19803000-19822000	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr17:19803000-19824400	Strong transcription	Fetal Muscle Trunk	muscle
47	chr17:19803000-19851800	Strong transcription	Fetal Thymus	thymus
48	chr17:19803200-19806800	Weak transcription	HepG2	liver
49	chr17:19803200-19840800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr17:19803400-19807000	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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