Variant report

Variant	rs203479
Chromosome Location	chr17:19829311-19829312
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19770914..19772634-chr17:19827559..19830080,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000083290	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 11 )

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	0.81[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	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1479129	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];0.89[YRI][hapmap];0.84[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]
rs1638526	0.83[YRI][hapmap]
rs166840	0.85[EUR][1000 genomes]
rs169412	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];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs169414	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs175921	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs175922	0.88[ASW][hapmap];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]
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	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203452	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203455	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs203456	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203457	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203458	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];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203459	0.87[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];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203461	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203462	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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203465	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203466	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]
rs203469	0.95[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]
rs203477	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	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203482	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2108978	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];0.84[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];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs427798	0.84[AFR][1000 genomes];0.84[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];0.93[YRI][hapmap];0.82[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	0.80[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];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8066150	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs850623	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];0.94[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];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.84[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs203479	SPECC1	Cis_1M	lymphoblastoid	RTeQTL
rs203479	AKAP10	cis	normal skin	skin_eQTL
rs203479	CYTSB	cis	cerebellum	SCAN
rs203479	AKAP10	cis	uninvolved skin	skin_eQTL
rs203479	AKAP10	cis	multi-tissue	Pritchard
rs203479	AKAP10	cis	lymphoblastoid	seeQTL
rs203479	TMEM11	cis	cerebellum	SCAN
rs203479	ALDH3A1	cis	parietal	SCAN
rs203479	SNORD49B	cis	parietal	SCAN
rs203479	AKAP10	cis	Lymphoblastoid	GTEx
rs203479	AKAP10	cis	lesional skin	skin_eQTL

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	chr17:19803600-19829800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:19803600-19845400	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr17:19803600-19848000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr17:19803800-19830800	Strong transcription	Primary B cells from peripheral blood	blood
10	chr17:19804000-19844400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr17:19804000-19853000	Strong transcription	Dnd41	blood
12	chr17:19806200-19844000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr17:19806200-19844600	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr17:19806400-19830200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr17:19806400-19846200	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr17:19807800-19843800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr17:19809200-19832200	Weak transcription	Fetal Brain Male	brain
18	chr17:19809400-19837400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr17:19810000-19830800	Strong transcription	Adipose Nuclei	Adipose
20	chr17:19810200-19836600	Weak transcription	Fetal Heart	heart
21	chr17:19811800-19834800	Weak transcription	Small Intestine	intestine
22	chr17:19812200-19845400	Strong transcription	Liver	Liver
23	chr17:19813200-19833800	Weak transcription	Pancreas	Pancrea
24	chr17:19815000-19838600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr17:19816800-19844400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr17:19817800-19844200	Weak transcription	Stomach Mucosa	stomach
27	chr17:19818200-19830600	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr17:19818200-19836400	Strong transcription	A549	lung
29	chr17:19818600-19839400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr17:19819600-19833600	Weak transcription	Brain Substantia Nigra	brain
31	chr17:19819600-19844600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr17:19819800-19833800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr17:19820000-19832200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr17:19821000-19831800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr17:19821000-19832200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr17:19821000-19833800	Weak transcription	Aorta	Aorta
37	chr17:19821000-19838000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr17:19821000-19842800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr17:19822000-19830200	Weak transcription	Lung	lung
40	chr17:19822000-19830200	Weak transcription	Spleen	Spleen
41	chr17:19822000-19832200	Weak transcription	Brain Angular Gyrus	brain
42	chr17:19822000-19832400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr17:19822000-19833600	Weak transcription	Gastric	stomach
44	chr17:19823000-19830200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr17:19823000-19832200	Weak transcription	Brain Hippocampus Middle	brain
46	chr17:19823000-19832200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr17:19823000-19833600	Weak transcription	Brain Germinal Matrix	brain
48	chr17:19823000-19833800	Weak transcription	Esophagus	oesophagus
49	chr17:19823400-19833200	Weak transcription	NHLF	lung
50	chr17:19823400-19837600	Weak transcription	Psoas Muscle	Psoas

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