Variant report

Variant	rs203466
Chromosome Location	chr17:19809953-19809954
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11204419	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204420	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[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];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[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];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1638525	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs166840	0.86[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];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs169414	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs175921	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[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];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860302	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs191865	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs203450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203451	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203452	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203455	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs203456	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[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];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203459	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[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];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203461	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[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];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[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];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203469	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203470	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203477	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]
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];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203482	0.99[AMR][1000 genomes];0.98[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];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[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];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs427798	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[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];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[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	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[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];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8066150	0.83[AMR][1000 genomes];0.85[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];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[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];0.95[AMR][1000 genomes];0.98[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	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9914273	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9914304	0.90[EUR][1000 genomes]
rs9916675	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs203466	TMEM11	cis	cerebellum	SCAN
rs203466	AKAP10	cis	normal skin	skin_eQTL
rs203466	AKAP10	cis	uninvolved skin	skin_eQTL
rs203466	AKAP10	cis	lymphoblastoid	seeQTL
rs203466	ALDH3A1	cis	parietal	SCAN
rs203466	AKAP10	cis	Lymphoblastoid	GTEx
rs203466	AKAP10	cis	multi-tissue	Pritchard
rs203466	SNORD49B	cis	parietal	SCAN
rs203466	AKAP10	cis	lesional skin	skin_eQTL
rs203466	CYTSB	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19801400-19814200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:19801600-19814600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr17:19802200-19814200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr17:19802800-19824000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr17:19802800-19829000	Strong transcription	Fetal Muscle Leg	muscle
6	chr17:19802800-19844400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr17:19802800-19846400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr17:19802800-19852400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr17:19803000-19810400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr17:19803000-19810400	Strong transcription	Stomach Smooth Muscle	stomach
11	chr17:19803000-19813200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr17:19803000-19822000	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr17:19803000-19824400	Strong transcription	Fetal Muscle Trunk	muscle
14	chr17:19803000-19851800	Strong transcription	Fetal Thymus	thymus
15	chr17:19803200-19840800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr17:19803600-19813400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr17:19803600-19814000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr17:19803600-19826200	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr17:19803600-19829800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr17:19803600-19845400	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr17:19803600-19848000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr17:19803800-19812000	Strong transcription	Fetal Intestine Small	intestine
23	chr17:19803800-19818000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr17:19803800-19822400	Strong transcription	Primary T cells from cord blood	blood
25	chr17:19803800-19823400	Strong transcription	Duodenum Mucosa	Duodenum
26	chr17:19803800-19824000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr17:19803800-19830800	Strong transcription	Primary B cells from peripheral blood	blood
28	chr17:19804000-19823600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr17:19804000-19844400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr17:19804000-19853000	Strong transcription	Dnd41	blood
31	chr17:19804200-19810600	Strong transcription	Primary B cells from cord blood	blood
32	chr17:19805400-19814200	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr17:19805600-19823800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr17:19805800-19824000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr17:19806200-19810400	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr17:19806200-19812000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr17:19806200-19844000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr17:19806200-19844600	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr17:19806400-19810200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr17:19806400-19812200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr17:19806400-19830200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr17:19806400-19846200	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr17:19806600-19810400	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr17:19806600-19810600	Strong transcription	Fetal Brain Female	brain
45	chr17:19806600-19813200	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr17:19806800-19810000	Strong transcription	GM12878-XiMat	blood
47	chr17:19806800-19810200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr17:19806800-19810400	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr17:19806800-19810600	Strong transcription	Hela-S3	cervix
50	chr17:19806800-19813400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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