Variant report

Variant	rs801534
Chromosome Location	chr7:18638652-18638653
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1089358	0.90[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1089359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1405618	1.00[JPT][hapmap]
rs1633775	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1726600	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]
rs1726602	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2254993	0.89[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs706084	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs706085	0.90[ASW][hapmap];0.89[CEU][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs801511	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs801512	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs801513	0.90[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs801519	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs801532	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs801535	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968841	0.89[CEU][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs968842	0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.83[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs801534	HDAC9	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:18614600-18640400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:18614600-18640400	Weak transcription	Spleen	Spleen
3	chr7:18614600-18644200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr7:18617000-18640400	Weak transcription	Brain Angular Gyrus	brain
5	chr7:18618400-18641000	Weak transcription	Psoas Muscle	Psoas
6	chr7:18621000-18640800	Weak transcription	Brain Hippocampus Middle	brain
7	chr7:18621000-18641200	Weak transcription	Right Ventricle	heart
8	chr7:18621200-18640200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:18621200-18646800	Weak transcription	HSMM	muscle
10	chr7:18621400-18639000	Weak transcription	Fetal Brain Female	brain
11	chr7:18621400-18641000	Weak transcription	Brain Anterior Caudate	brain
12	chr7:18621800-18643600	Weak transcription	Brain Germinal Matrix	brain
13	chr7:18622000-18641000	Weak transcription	Brain Substantia Nigra	brain
14	chr7:18623800-18640200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr7:18627400-18639200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr7:18628000-18640800	Weak transcription	HMEC	breast
17	chr7:18628600-18640400	Weak transcription	NHEK	skin
18	chr7:18630000-18640400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr7:18630200-18640000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr7:18630200-18640400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr7:18630400-18640000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr7:18630600-18640400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr7:18631000-18640400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr7:18631600-18640200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr7:18632000-18640400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr7:18632000-18640800	Weak transcription	NH-A	brain
27	chr7:18633000-18640600	Weak transcription	Osteobl	bone
28	chr7:18633000-18645400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr7:18633800-18639000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr7:18633800-18639800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:18633800-18640000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr7:18633800-18640200	Strong transcription	Primary B cells from peripheral blood	blood
33	chr7:18633800-18640200	Weak transcription	Left Ventricle	heart
34	chr7:18633800-18641000	Weak transcription	Fetal Muscle Leg	muscle
35	chr7:18633800-18647000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr7:18633800-18650000	Weak transcription	Aorta	Aorta
37	chr7:18634000-18640600	Weak transcription	Adipose Nuclei	Adipose
38	chr7:18634000-18640800	Weak transcription	HSMMtube	muscle
39	chr7:18634200-18639000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr7:18635000-18640000	Strong transcription	Primary B cells from cord blood	blood
41	chr7:18635600-18640400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr7:18636200-18639200	Strong transcription	Primary hematopoietic stem cells	blood
43	chr7:18636600-18640000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr7:18636800-18639200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr7:18636800-18639200	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr7:18637000-18640000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr7:18637000-18640000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr7:18637400-18639600	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr7:18637800-18640000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr7:18637800-18640200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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