Variant report

Variant	rs1726600
Chromosome Location	chr7:18648659-18648660
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1089358	0.80[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1089359	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1405618	1.00[JPT][hapmap]
rs1633775	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1726602	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2254993	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs706084	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs706085	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs801511	0.80[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs801512	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs801513	0.80[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs801519	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs801531	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs801532	1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs801534	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs801535	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs968841	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs968842	0.89[CEU][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755157	chr7:18337660-18805860	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv830917	chr7:18612436-18817712	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1726600	HDAC9	cis	parietal	SCAN
rs1726600	HDAC9	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:18633800-18650000	Weak transcription	Aorta	Aorta
2	chr7:18641200-18670800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr7:18641400-18663400	Weak transcription	Brain Angular Gyrus	brain
4	chr7:18641400-18687600	Weak transcription	Fetal Heart	heart
5	chr7:18644800-18666600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:18644800-18678000	Weak transcription	Fetal Brain Male	brain
7	chr7:18645200-18648800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr7:18645200-18652000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr7:18645200-18653800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr7:18645200-18654000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr7:18645200-18659000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr7:18645200-18677800	Weak transcription	NHDF-Ad	bronchial
13	chr7:18645200-18678200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr7:18645200-18687200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr7:18645200-18708000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr7:18645400-18649000	Weak transcription	Right Ventricle	heart
17	chr7:18645400-18661600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr7:18645400-18662400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr7:18645400-18686600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr7:18645400-18687400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr7:18645400-18687800	Weak transcription	Brain Hippocampus Middle	brain
22	chr7:18645400-18721000	Weak transcription	Psoas Muscle	Psoas
23	chr7:18645600-18676800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr7:18645800-18659000	Weak transcription	HSMMtube	muscle
25	chr7:18645800-18662800	Weak transcription	Brain Germinal Matrix	brain
26	chr7:18645800-18663200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr7:18645800-18663400	Weak transcription	Left Ventricle	heart
28	chr7:18645800-18684400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr7:18645800-18687400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr7:18645800-18687400	Weak transcription	Fetal Muscle Leg	muscle
31	chr7:18645800-18706000	Weak transcription	HMEC	breast
32	chr7:18646000-18658800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr7:18646000-18674000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr7:18646000-18678000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr7:18646000-18678000	Weak transcription	Fetal Brain Female	brain
36	chr7:18646000-18687400	Weak transcription	NHEK	skin
37	chr7:18646000-18692400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr7:18647000-18657800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr7:18647000-18661400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr7:18647200-18665600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr7:18647200-18665800	Weak transcription	HSMM	muscle
42	chr7:18647200-18687800	Weak transcription	NH-A	brain
43	chr7:18648400-18649200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr7:18648600-18650600	Strong transcription	Primary B cells from cord blood	blood

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