Variant report

Variant	rs17604987
Chromosome Location	chr17:19867331-19867332
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:19865047..19867496-chr17:19877970..19881173,3	K562	blood:
2	chr17:19864763..19867496-chr17:19878736..19880749,2	K562	blood:
3	chr17:19861521..19863137-chr17:19866013..19868879,2	MCF-7	breast:
4	chr17:19866196..19868366-chr17:19868969..19871678,2	K562	blood:
5	chr17:19867234..19871590-chr17:19877670..19882500,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108599	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1009082	1.00[CHB][hapmap]
rs10438824	1.00[CHB][hapmap]
rs12449662	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12450857	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12453720	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];0.84[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12943369	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12944084	0.85[AMR][1000 genomes];0.80[EUR][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];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1638527	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1638528	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs169413	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17605101	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17668529	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17686622	1.00[CHB][hapmap]
rs17686839	1.00[CHB][hapmap]
rs17759609	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs1812934	1.00[CHB][hapmap]
rs203449	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs203454	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs203464	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs203467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs203474	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs203475	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]
rs203476	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs203478	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs203480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2108981	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34089239	1.00[CHB][hapmap]
rs34182788	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34726000	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35254155	0.81[AMR][1000 genomes]
rs35315252	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35925051	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35979784	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36097967	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862151	1.00[CHB][hapmap]
rs403021	0.89[EUR][1000 genomes]
rs427033	0.95[CEU][hapmap];0.87[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];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4925055	0.83[AMR][1000 genomes]
rs4925063	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925064	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925084	1.00[CHB][hapmap]
rs56005410	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066267	0.81[AMR][1000 genomes]
rs62066345	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62066346	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066347	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066348	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066349	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066350	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066351	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066352	0.81[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];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7209653	0.87[CEU][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8079923	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs850622	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9891503	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9901294	0.87[CEU][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.88[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
rs17604987	AKAP10	cis	lymphoblastoid	seeQTL
rs17604987	AKAP10	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19840000-19879200	Weak transcription	Fetal Brain Male	brain
2	chr17:19846800-19875600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr17:19850600-19879200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr17:19850600-19880200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr17:19850600-19880200	Weak transcription	Aorta	Aorta
6	chr17:19851600-19871600	Weak transcription	Colonic Mucosa	Colon
7	chr17:19852000-19871000	Weak transcription	Small Intestine	intestine
8	chr17:19852200-19879400	Weak transcription	Esophagus	oesophagus
9	chr17:19852200-19879600	Weak transcription	Right Ventricle	heart
10	chr17:19852200-19880000	Weak transcription	Psoas Muscle	Psoas
11	chr17:19852800-19869800	Weak transcription	Fetal Heart	heart
12	chr17:19857000-19868800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr17:19857200-19875000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr17:19857400-19873800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr17:19857400-19880400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:19857600-19874000	Strong transcription	Dnd41	blood
17	chr17:19857600-19874400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr17:19857600-19875200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr17:19857600-19880200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr17:19858400-19873600	Strong transcription	Duodenum Mucosa	Duodenum
21	chr17:19858600-19874400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr17:19858600-19875800	Strong transcription	Primary B cells from cord blood	blood
23	chr17:19859000-19877200	Strong transcription	Fetal Thymus	thymus
24	chr17:19859200-19870800	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr17:19859200-19874400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr17:19859200-19875600	Strong transcription	Placenta	Placenta
27	chr17:19859200-19878600	Strong transcription	Primary B cells from peripheral blood	blood
28	chr17:19859600-19876800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr17:19859800-19879400	Weak transcription	Brain Angular Gyrus	brain
30	chr17:19861000-19875600	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr17:19861600-19869800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr17:19861800-19867800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr17:19861800-19868200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr17:19861800-19870800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr17:19861800-19870800	Weak transcription	Pancreas	Pancrea
36	chr17:19861800-19873000	Weak transcription	Gastric	stomach
37	chr17:19861800-19878600	Weak transcription	Colon Smooth Muscle	Colon
38	chr17:19861800-19880000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr17:19862000-19867600	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr17:19862000-19868000	Weak transcription	K562	blood
41	chr17:19862000-19871400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr17:19862000-19876800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr17:19862000-19879000	Weak transcription	Brain Substantia Nigra	brain
44	chr17:19862000-19879200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr17:19862000-19880200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr17:19862000-19880200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr17:19862200-19868400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr17:19862200-19880000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr17:19862400-19867600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr17:19862400-19868200	Weak transcription	NHEK	skin

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