Variant report

Variant	rs203477
Chromosome Location	chr17:19831819-19831820
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11204419	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204420	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204421	0.82[ASN][1000 genomes]
rs119672	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1479129	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1638525	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs166840	0.85[EUR][1000 genomes]
rs169412	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs169414	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs175921	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs175922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860302	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs191865	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2013443	0.82[YRI][hapmap]
rs203450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203451	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203452	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203455	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs203456	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203457	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203458	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203459	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs203460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203461	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203462	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203465	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203466	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203469	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203470	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203479	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203481	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203482	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2108978	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35003563	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs397969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs427798	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4924803	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs4925060	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4925065	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs4925072	0.88[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs4925077	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs4925081	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs56153261	0.86[ASN][1000 genomes]
rs6587206	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7207625	0.87[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs7208025	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs7208365	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs7209734	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs7222403	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8066150	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs850623	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888423	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs918227	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs9899357	0.84[CEU][hapmap];0.80[GIH][hapmap];0.90[TSI][hapmap]
rs9907752	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9914273	1.00[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9914304	0.89[EUR][1000 genomes]
rs9916675	0.81[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs203477	SNORD49B	cis	parietal	SCAN
rs203477	SPECC1	Cis_1M	lymphoblastoid	RTeQTL
rs203477	AKAP10	cis	lymphoblastoid	seeQTL
rs203477	TMEM11	cis	cerebellum	SCAN
rs203477	ALDH3A1	cis	parietal	SCAN
rs203477	CYTSB	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19802800-19844400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr17:19802800-19846400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr17:19802800-19852400	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr17:19803000-19851800	Strong transcription	Fetal Thymus	thymus
5	chr17:19803200-19840800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr17:19803600-19845400	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr17:19803600-19848000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr17:19804000-19844400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr17:19804000-19853000	Strong transcription	Dnd41	blood
10	chr17:19806200-19844000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr17:19806200-19844600	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr17:19806400-19846200	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr17:19807800-19843800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr17:19809200-19832200	Weak transcription	Fetal Brain Male	brain
15	chr17:19809400-19837400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr17:19810200-19836600	Weak transcription	Fetal Heart	heart
17	chr17:19811800-19834800	Weak transcription	Small Intestine	intestine
18	chr17:19812200-19845400	Strong transcription	Liver	Liver
19	chr17:19813200-19833800	Weak transcription	Pancreas	Pancrea
20	chr17:19815000-19838600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr17:19816800-19844400	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr17:19817800-19844200	Weak transcription	Stomach Mucosa	stomach
23	chr17:19818200-19836400	Strong transcription	A549	lung
24	chr17:19818600-19839400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr17:19819600-19833600	Weak transcription	Brain Substantia Nigra	brain
26	chr17:19819600-19844600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr17:19819800-19833800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr17:19820000-19832200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr17:19821000-19832200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr17:19821000-19833800	Weak transcription	Aorta	Aorta
31	chr17:19821000-19838000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr17:19821000-19842800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr17:19822000-19832200	Weak transcription	Brain Angular Gyrus	brain
34	chr17:19822000-19832400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr17:19822000-19833600	Weak transcription	Gastric	stomach
36	chr17:19823000-19832200	Weak transcription	Brain Hippocampus Middle	brain
37	chr17:19823000-19832200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr17:19823000-19833600	Weak transcription	Brain Germinal Matrix	brain
39	chr17:19823000-19833800	Weak transcription	Esophagus	oesophagus
40	chr17:19823400-19833200	Weak transcription	NHLF	lung
41	chr17:19823400-19837600	Weak transcription	Psoas Muscle	Psoas
42	chr17:19823600-19832200	Weak transcription	NH-A	brain
43	chr17:19823600-19836600	Weak transcription	HMEC	breast
44	chr17:19823800-19832200	Weak transcription	HSMM	muscle
45	chr17:19824400-19840200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr17:19824800-19840400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr17:19824800-19844200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr17:19824800-19845800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr17:19825000-19843600	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr17:19825000-19845200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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