Variant report

Variant	rs6813
Chromosome Location	chr17:19808445-19808446
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:19806568..19809445-chr17:20006913..20008589,2	K562	blood:
2	chr17:19769508..19771836-chr17:19806966..19809532,3	MCF-7	breast:
3	chr17:19803045..19804628-chr17:19806537..19808845,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ULK2-5	chr17:19808236-19808519	expReg_chr17_3232_-

Variant related genes	Relation type
ENSG00000083290	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12450857	0.86[CEU][hapmap];0.81[AMR][1000 genomes]
rs12453720	0.86[CEU][hapmap];0.86[GIH][hapmap];0.81[AMR][1000 genomes]
rs12943369	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1638526	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1638527	0.95[CEU][hapmap];0.96[GIH][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1638528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs169413	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17604987	0.95[CEU][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17605101	0.82[EUR][1000 genomes]
rs17668529	0.80[AMR][1000 genomes]
rs203449	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203454	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203464	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203467	0.95[CEU][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs203474	0.93[EUR][1000 genomes]
rs203475	0.95[CEU][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs203476	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs203478	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs203480	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2108981	0.86[CEU][hapmap];0.93[GIH][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34182788	0.80[AMR][1000 genomes]
rs34726000	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35925051	0.82[EUR][1000 genomes]
rs36097967	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs403021	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs427033	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4925054	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4925055	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4925064	0.80[AMR][1000 genomes]
rs56005410	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62066267	0.83[AMR][1000 genomes]
rs62066348	0.80[AMR][1000 genomes]
rs62066349	0.80[AMR][1000 genomes]
rs62066350	0.80[AMR][1000 genomes]
rs62066351	0.80[AMR][1000 genomes]
rs7209653	0.94[ASW][hapmap];0.91[CEU][hapmap];0.96[GIH][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8079923	0.95[CEU][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs850622	0.95[CEU][hapmap];0.96[GIH][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9891503	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9901294	0.94[ASW][hapmap];0.91[CEU][hapmap];0.96[GIH][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
4	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6813	AKAP10	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 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	chr17:19801400-19808600	Weak transcription	Colonic Mucosa	Colon
3	chr17:19801400-19808600	Weak transcription	Small Intestine	intestine
4	chr17:19801400-19809000	Weak transcription	Psoas Muscle	Psoas
5	chr17:19801400-19814200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr17:19801600-19808800	Weak transcription	Fetal Heart	heart
7	chr17:19801600-19808800	Weak transcription	K562	blood
8	chr17:19801600-19814600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr17:19802200-19809000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr17:19802200-19814200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr17:19802800-19824000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr17:19802800-19829000	Strong transcription	Fetal Muscle Leg	muscle
13	chr17:19802800-19844400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr17:19802800-19846400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr17:19802800-19852400	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr17:19803000-19810400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr17:19803000-19810400	Strong transcription	Stomach Smooth Muscle	stomach
18	chr17:19803000-19813200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr17:19803000-19822000	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr17:19803000-19824400	Strong transcription	Fetal Muscle Trunk	muscle
21	chr17:19803000-19851800	Strong transcription	Fetal Thymus	thymus
22	chr17:19803200-19840800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr17:19803600-19809000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr17:19803600-19813400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr17:19803600-19814000	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr17:19803600-19826200	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr17:19803600-19829800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr17:19803600-19845400	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr17:19803600-19848000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr17:19803800-19812000	Strong transcription	Fetal Intestine Small	intestine
31	chr17:19803800-19818000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr17:19803800-19822400	Strong transcription	Primary T cells from cord blood	blood
33	chr17:19803800-19823400	Strong transcription	Duodenum Mucosa	Duodenum
34	chr17:19803800-19824000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr17:19803800-19830800	Strong transcription	Primary B cells from peripheral blood	blood
36	chr17:19804000-19809000	Strong transcription	Adipose Nuclei	Adipose
37	chr17:19804000-19823600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr17:19804000-19844400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr17:19804000-19853000	Strong transcription	Dnd41	blood
40	chr17:19804200-19810600	Strong transcription	Primary B cells from cord blood	blood
41	chr17:19804600-19809800	Weak transcription	Aorta	Aorta
42	chr17:19805400-19814200	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr17:19805600-19823800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr17:19805800-19824000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr17:19806200-19810400	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr17:19806200-19812000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr17:19806200-19844000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr17:19806200-19844600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr17:19806400-19810200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr17:19806400-19812200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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