Variant report

Variant	rs17756179
Chromosome Location	chr9:26959914-26959915
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:26907670..26910296-chr9:26959042..26961750,2	K562	blood:
2	chr9:26955666..26957510-chr9:26957953..26960987,3	MCF-7	breast:
3	chr9:26951108..26953952-chr9:26958227..26960200,3	K562	blood:

Variant related genes	Relation type
ENSG00000234676	Chromatin interaction
ENSG00000096872	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10511792	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511794	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511795	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511797	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12353269	1.00[JPT][hapmap]
rs1336332	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs1541145	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16910873	0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17694127	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs17694324	0.83[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17694499	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17694631	0.86[AFR][1000 genomes]
rs17756299	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2184740	0.86[EUR][1000 genomes]
rs3429	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs57890470	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59100252	0.98[EUR][1000 genomes]
rs59175724	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60130669	0.80[AFR][1000 genomes]
rs62542660	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62542663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62542665	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62542666	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62542667	0.95[AFR][1000 genomes]
rs62542669	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62542670	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62542672	0.90[AFR][1000 genomes]
rs62542704	0.90[AFR][1000 genomes]
rs62542705	0.86[AFR][1000 genomes]
rs62542706	0.86[AFR][1000 genomes]
rs62542707	0.86[AFR][1000 genomes]
rs62542708	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62544403	0.81[EUR][1000 genomes]
rs62544411	1.00[ASN][1000 genomes]
rs62544412	1.00[ASN][1000 genomes]
rs62544413	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62544434	1.00[ASN][1000 genomes]
rs62544435	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62544437	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62544440	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62544453	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62546682	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62546683	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62546685	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7018962	0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7030424	1.00[YRI][hapmap]
rs7036055	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs7036871	0.91[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7038875	0.80[AFR][1000 genomes]
rs7044910	0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs73433937	0.86[EUR][1000 genomes]
rs73436012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73436044	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73436047	0.95[AFR][1000 genomes]
rs73438223	0.90[AFR][1000 genomes]
rs73438278	0.80[AFR][1000 genomes]
rs73438282	0.80[AFR][1000 genomes]
rs73438302	0.80[AFR][1000 genomes]
rs73440204	0.80[AFR][1000 genomes]
rs73440205	0.80[AFR][1000 genomes]
rs73440214	0.80[AFR][1000 genomes]
rs73440217	0.80[AFR][1000 genomes]
rs7865596	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865919	0.80[AFR][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	nsv528614	chr9:26893662-27074233	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv517269	chr9:26945976-27137242	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv892862	chr9:26956663-27190655	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17756179	CAAP1	cis	Artery Tibial	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26957000-26961800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:26957000-26973800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr9:26957000-26980800	Weak transcription	Lung	lung
4	chr9:26957000-26983200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:26957000-26984400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr9:26957000-27024000	Weak transcription	Esophagus	oesophagus
7	chr9:26957200-26961400	Weak transcription	Brain Substantia Nigra	brain
8	chr9:26957200-26961600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr9:26957200-26961800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:26957200-26961800	Weak transcription	HSMM	muscle
11	chr9:26957200-26962000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr9:26957200-26962200	Weak transcription	Thymus	Thymus
13	chr9:26957200-26976000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:26957200-26980800	Weak transcription	Fetal Intestine Large	intestine
15	chr9:26957200-26980800	Weak transcription	Fetal Stomach	stomach
16	chr9:26957200-26982600	Weak transcription	Fetal Muscle Leg	muscle
17	chr9:26957200-26982600	Weak transcription	Left Ventricle	heart
18	chr9:26957200-26983200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr9:26957200-26983200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr9:26957200-26984400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr9:26957200-26984400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr9:26957200-26984600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr9:26957200-26984800	Weak transcription	Primary B cells from cord blood	blood
24	chr9:26957200-26984800	Weak transcription	Fetal Thymus	thymus
25	chr9:26957200-27026600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr9:26957200-27040000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr9:26957400-26961800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr9:26957400-26962000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr9:26957400-26962000	Weak transcription	Liver	Liver
30	chr9:26957400-26962200	Weak transcription	Fetal Lung	lung
31	chr9:26957400-26963800	Weak transcription	NHLF	lung
32	chr9:26957400-26964800	Weak transcription	Primary T cells from cord blood	blood
33	chr9:26957400-26974800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr9:26957400-26978200	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr9:26957400-26980800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr9:26957400-26982800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr9:26957400-26983200	Weak transcription	Brain Anterior Caudate	brain
38	chr9:26957400-26983400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr9:26957400-26984600	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr9:26957600-26961400	Weak transcription	GM12878-XiMat	blood
41	chr9:26957600-26961600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr9:26957600-26961800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr9:26957600-26962000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr9:26957600-26965800	Weak transcription	Fetal Brain Female	brain
45	chr9:26957600-26975200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr9:26957600-26979400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr9:26957600-26982800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr9:26957600-26983200	Weak transcription	Fetal Kidney	kidney
49	chr9:26957600-26983400	Weak transcription	Brain Angular Gyrus	brain
50	chr9:26957600-26984800	Weak transcription	Brain Hippocampus Middle	brain

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