Variant report

Variant	rs203475
Chromosome Location	chr17:19850975-19850976
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs12449662	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12450857	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12453720	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12943369	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12944084	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12946508	0.87[ASN][1000 genomes]
rs12947950	1.00[CHB][hapmap]
rs12949485	1.00[CHB][hapmap]
rs1638526	0.95[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1638527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1638528	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs169413	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17604987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17605101	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17668529	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17686622	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17686839	1.00[CHB][hapmap]
rs17759609	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1812934	1.00[CHB][hapmap]
rs203449	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs203454	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs203464	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs203467	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs203474	1.00[EUR][1000 genomes]
rs203476	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs203478	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs203480	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2108981	0.86[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[LWK][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34182788	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34726000	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35315252	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35925051	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35979784	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36097967	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862151	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs403021	0.90[EUR][1000 genomes]
rs427033	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs4577147	0.87[ASN][1000 genomes]
rs4588033	1.00[CHB][hapmap]
rs4924802	1.00[CHB][hapmap]
rs4924809	1.00[CHB][hapmap]
rs4925054	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs4925055	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4925063	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925064	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925084	1.00[CHB][hapmap]
rs56005410	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066345	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62066346	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066347	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066348	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066349	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066350	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066351	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066352	0.80[AMR][1000 genomes]
rs62067482	0.87[ASN][1000 genomes]
rs62067483	0.87[ASN][1000 genomes]
rs6813	0.95[CEU][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7209653	0.87[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8079923	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs850622	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9891503	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9901294	0.87[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs203475	SPECC1	Cis_1M	lymphoblastoid	RTeQTL
rs203475	AKAP10	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19802800-19852400	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr17:19803000-19851800	Strong transcription	Fetal Thymus	thymus
3	chr17:19804000-19853000	Strong transcription	Dnd41	blood
4	chr17:19825200-19851800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:19827600-19851600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr17:19827600-19852800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr17:19830600-19851200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:19831600-19851400	Strong transcription	Primary B cells from peripheral blood	blood
9	chr17:19838600-19851600	Weak transcription	Psoas Muscle	Psoas
10	chr17:19840000-19851600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr17:19840000-19879200	Weak transcription	Fetal Brain Male	brain
12	chr17:19841600-19852800	Strong transcription	Primary B cells from cord blood	blood
13	chr17:19841800-19851600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr17:19841800-19852600	Strong transcription	Fetal Intestine Large	intestine
15	chr17:19842000-19852600	Strong transcription	Hela-S3	cervix
16	chr17:19842400-19851800	Strong transcription	Primary hematopoietic stem cells	blood
17	chr17:19842600-19851600	Strong transcription	GM12878-XiMat	blood
18	chr17:19844600-19851400	Weak transcription	Brain Substantia Nigra	brain
19	chr17:19844600-19851600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr17:19844600-19851800	Weak transcription	Small Intestine	intestine
21	chr17:19844600-19859200	Weak transcription	NHDF-Ad	bronchial
22	chr17:19844800-19851000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr17:19844800-19851600	Weak transcription	Fetal Heart	heart
24	chr17:19844800-19853000	Strong transcription	HepG2	liver
25	chr17:19844800-19859600	Weak transcription	HSMMtube	muscle
26	chr17:19844800-19861000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr17:19845200-19857200	Weak transcription	Fetal Kidney	kidney
28	chr17:19845400-19857000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr17:19846000-19852200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr17:19846200-19851000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr17:19846200-19852000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr17:19846200-19852000	Strong transcription	Fetal Muscle Trunk	muscle
33	chr17:19846400-19851600	Strong transcription	Fetal Muscle Leg	muscle
34	chr17:19846400-19851600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr17:19846400-19851800	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr17:19846400-19852200	Strong transcription	Liver	Liver
37	chr17:19846400-19852400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr17:19846600-19851600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr17:19846600-19851600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr17:19846600-19852600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr17:19846800-19851400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr17:19846800-19851600	Strong transcription	HSMM	muscle
43	chr17:19846800-19852000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr17:19846800-19875600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr17:19847000-19851000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr17:19847000-19851400	Strong transcription	Adipose Nuclei	Adipose
47	chr17:19847200-19851800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr17:19847200-19852000	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr17:19847200-19852200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr17:19847400-19851800	Strong transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links