Variant report

Variant	rs397969
Chromosome Location	chr17:19804247-19804248
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:19799931-19805138	K562	blood:	n/a	n/a
2	FOS	chr17:19804191-19804468	MCF10A-Er-Src	breast:	n/a	n/a
3	FOXA1	chr17:19804083-19804458	T-47D	breast:	n/a	chr17:19804293-19804308
4	SIN3AK20	chr17:19803964-19804673	MCF-7	breast:	n/a	n/a
5	POLR2A	chr17:19804110-19804268	H1-hESC	embryonic stem cell:	n/a	n/a
6	FOS	chr17:19804225-19804501	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr17:19803967-19804597	GM12878	blood:	n/a	n/a
8	MYC	chr17:19804100-19804425	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr17:19803598-19804675	Hela-S3	cervix:	n/a	n/a
10	FOXA2	chr17:19804053-19804626	A549	lung:	n/a	n/a
11	TFAP2A	chr17:19804083-19804585	Hela-S3	cervix:	n/a	chr17:19804383-19804398 chr17:19804384-19804396 chr17:19804384-19804396 chr17:19804384-19804396 chr17:19804384-19804396
12	FOXA2	chr17:19804002-19804623	A549	lung:	n/a	n/a
13	POLR2A	chr17:19804113-19804407	Hela-S3	cervix:	n/a	n/a
14	TFAP2C	chr17:19804054-19804584	Hela-S3	cervix:	n/a	chr17:19804381-19804396
15	FOXA1	chr17:19804073-19804507	T-47D	breast:	n/a	chr17:19804293-19804308
16	POLR2A	chr17:19803854-19804498	HepG2	liver:	n/a	n/a
17	POLR2A	chr17:19803683-19804578	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:19768657..19772126-chr17:19801455..19804744,3	MCF-7	breast:
2	chr17:19803045..19804628-chr17:19806537..19808845,2	K562	blood:
3	chr17:19748663..19750741-chr17:19801498..19804267,2	K562	blood:
4	chr17:19769802..19772027-chr17:19799780..19804333,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270091	TF binding region
ENSG00000083290	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11204419	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11204420	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs119672	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1479129	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];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1638525	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs166840	0.88[EUR][1000 genomes]
rs169412	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];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs169414	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs175921	0.80[EUR][1000 genomes];0.86[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];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1860302	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs191865	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs203450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203451	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203452	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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];0.93[ASN][1000 genomes]
rs203457	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];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203459	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs203460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203461	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203462	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];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203465	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];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs203466	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]
rs203469	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203470	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203477	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]
rs203479	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]
rs203481	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[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]
rs203482	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2108978	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];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35003563	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs427798	0.88[AMR][1000 genomes];0.96[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];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[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	0.91[ASN][1000 genomes]
rs6587206	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[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];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8066150	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs850623	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];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs860335	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];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[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];0.81[EUR][1000 genomes]
rs9907752	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9914273	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9914304	0.93[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	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	nsv518888	chr17:19789453-19804247	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	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

Variant related diseases (count:1)

Disease	PMID	Source
Platelet counts	22139419	GWAS catalog

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs397969	AKAP10	cis	Lymphoblastoid	GTEx
rs397969	AKAP10	cis	multi-tissue	Pritchard
rs397969	AKAP10	cis	lesional skin	skin_eQTL
rs397969	AKAP10	cis	lymphoblastoid	seeQTL
rs397969	CYTSB	cis	cerebellum	SCAN
rs397969	SPECC1	Cis_1M	lymphoblastoid	RTeQTL
rs397969	TMEM11	cis	cerebellum	SCAN
rs397969	AKAP10	cis	normal skin	skin_eQTL
rs397969	AKAP10	cis	uninvolved skin	skin_eQTL
rs397969	ALDH3A1	cis	parietal	SCAN
rs397969	SNORD49B	cis	parietal	SCAN

Chromatin state (count:119 , 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	chr17:19799400-19805000	Weak transcription	Fetal Intestine Large	intestine
4	chr17:19799800-19805200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr17:19799800-19806800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr17:19799800-19807000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr17:19800600-19807600	Weak transcription	Brain Angular Gyrus	brain
8	chr17:19801000-19808200	Weak transcription	Left Ventricle	heart
9	chr17:19801000-19808400	Weak transcription	Esophagus	oesophagus
10	chr17:19801400-19805400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr17:19801400-19806000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr17:19801400-19806600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr17:19801400-19806800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr17:19801400-19808200	Weak transcription	Right Ventricle	heart
15	chr17:19801400-19808400	Weak transcription	Fetal Kidney	kidney
16	chr17:19801400-19808400	Weak transcription	Gastric	stomach
17	chr17:19801400-19808400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr17:19801400-19808600	Weak transcription	Colonic Mucosa	Colon
19	chr17:19801400-19808600	Weak transcription	Small Intestine	intestine
20	chr17:19801400-19809000	Weak transcription	Psoas Muscle	Psoas
21	chr17:19801400-19814200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr17:19801600-19805600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr17:19801600-19806200	Weak transcription	Brain Germinal Matrix	brain
24	chr17:19801600-19806400	Weak transcription	Colon Smooth Muscle	Colon
25	chr17:19801600-19808400	Weak transcription	Brain Anterior Caudate	brain
26	chr17:19801600-19808400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr17:19801600-19808800	Weak transcription	Fetal Heart	heart
28	chr17:19801600-19808800	Weak transcription	K562	blood
29	chr17:19801600-19814600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr17:19802000-19806800	Weak transcription	NH-A	brain
31	chr17:19802000-19808400	Weak transcription	NHEK	skin
32	chr17:19802200-19806200	Weak transcription	HSMMtube	muscle
33	chr17:19802200-19806400	Weak transcription	NHDF-Ad	bronchial
34	chr17:19802200-19806600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr17:19802200-19806800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr17:19802200-19807400	Weak transcription	HUVEC	blood vessel
37	chr17:19802200-19809000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr17:19802200-19814200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr17:19802600-19806800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr17:19802600-19806800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr17:19802800-19804600	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr17:19802800-19804600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr17:19802800-19804600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr17:19802800-19805600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr17:19802800-19807600	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr17:19802800-19824000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr17:19802800-19829000	Strong transcription	Fetal Muscle Leg	muscle
48	chr17:19802800-19844400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr17:19802800-19846400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr17:19802800-19852400	Strong transcription	Primary neutrophils fromperipheralblood	blood

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