Variant report

Variant	rs2041409
Chromosome Location	chr7:14874381-14874382
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10085416	0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10085569	0.99[ASN][1000 genomes]
rs10225316	0.88[EUR][1000 genomes]
rs10241696	0.98[ASN][1000 genomes]
rs10276530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10487781	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1988291	0.87[EUR][1000 genomes]
rs2109499	0.85[ASN][1000 genomes]
rs2109500	0.82[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2191481	0.83[ASN][1000 genomes]
rs2191482	0.94[ASN][1000 genomes]
rs2358070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34561304	0.88[EUR][1000 genomes]
rs4721382	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58021112	0.88[EUR][1000 genomes]
rs60142008	0.87[EUR][1000 genomes]
rs60557254	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6461137	0.85[ASN][1000 genomes]
rs6461140	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7784739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790062	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7793794	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7806933	0.85[ASN][1000 genomes]
rs929522	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929523	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs994369	0.85[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	nsv1031041	chr7:14624127-14999201	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv538741	chr7:14624127-14999201	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2041409	HDAC9	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:14872400-14876000	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr7:14872400-14876000	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr7:14872400-14877000	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr7:14872400-14877600	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr7:14872800-14875800	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr7:14872800-14877000	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr7:14873000-14874800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr7:14873200-14874400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:14873200-14875400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:14873200-14875800	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr7:14873200-14876200	Enhancers	Brain Germinal Matrix	brain
12	chr7:14873200-14876600	Enhancers	H9 Cell Line	embryonic stem cell
13	chr7:14873200-14876600	Enhancers	NHDF-Ad	bronchial
14	chr7:14873200-14877600	Enhancers	Placenta Amnion	Placenta Amnion
15	chr7:14873400-14877000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:14873400-14881200	Weak transcription	NHLF	lung
17	chr7:14873600-14875000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr7:14873600-14875000	Weak transcription	Fetal Brain Female	brain
19	chr7:14873600-14877200	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr7:14873800-14874400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr7:14873800-14875200	Weak transcription	Fetal Brain Male	brain
22	chr7:14873800-14876000	Enhancers	HSMMtube	muscle
23	chr7:14874000-14874400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr7:14874000-14874400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr7:14874000-14874400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr7:14874000-14874400	Enhancers	Brain Anterior Caudate	brain
27	chr7:14874000-14874400	Enhancers	Fetal Muscle Leg	muscle
28	chr7:14874000-14874400	Enhancers	NH-A	brain
29	chr7:14874000-14874600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr7:14874000-14875000	Flanking Active TSS	Fetal Heart	heart
31	chr7:14874000-14876000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr7:14874000-14877000	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr7:14874000-14877600	Enhancers	H1 Cell Line	embryonic stem cell
34	chr7:14874200-14874400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr7:14874200-14874400	Enhancers	Muscle Satellite Cultured Cells	--
36	chr7:14874200-14874600	Enhancers	Brain Angular Gyrus	brain
37	chr7:14874200-14874800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr7:14874200-14876200	Enhancers	Hela-S3	cervix
39	chr7:14874200-14876200	Enhancers	Osteobl	bone

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