Variant report

Variant	rs12076649
Chromosome Location	chr1:228886709-228886710
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1006797	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10489542	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1108502	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12059178	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12066510	1.00[CEU][hapmap]
rs12070785	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12077418	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12078927	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12092986	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12096381	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1535129	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2009564	0.87[EUR][1000 genomes]
rs2180162	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2207704	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2295255	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34036301	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3806285	0.82[JPT][hapmap];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3820265	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4654625	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4654723	0.85[CEU][hapmap]
rs6665140	1.00[CEU][hapmap]
rs6667385	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6681268	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6692721	0.85[CEU][hapmap]
rs7532644	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7547333	1.00[CEU][hapmap]
rs7554565	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013051	chr1:228786702-228903706	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv997801	chr1:228786702-228975127	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv870365	chr1:228788356-229267904	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv998255	chr1:228791784-228919202	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv549299	chr1:228793246-229455876	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv468316	chr1:228854703-228919202	Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv549300	chr1:228854703-228919202	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12076649	DUSP5P	cis	parietal	SCAN
rs12076649	TRIM17	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228877200-228889600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:228879200-228889600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:228880400-228889400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:228880600-228889400	Weak transcription	Brain Anterior Caudate	brain
5	chr1:228880600-228889600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:228880600-228889600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:228880600-228890400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:228881000-228886800	Weak transcription	HepG2	liver
9	chr1:228881000-228889200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:228881000-228889600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:228881200-228889600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:228881600-228889600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:228882600-228887600	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr1:228882800-228889200	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:228882800-228889400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:228882800-228889400	Weak transcription	Brain Substantia Nigra	brain
17	chr1:228882800-228889600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:228883000-228887800	Weak transcription	Spleen	Spleen
19	chr1:228883000-228889400	Weak transcription	Fetal Lung	lung
20	chr1:228883000-228889600	Weak transcription	Adipose Nuclei	Adipose
21	chr1:228883000-228889600	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:228883000-228893600	Weak transcription	Liver	Liver
23	chr1:228883200-228887400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr1:228883400-228887400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr1:228883400-228887400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:228883400-228887600	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr1:228883400-228889200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:228883800-228887600	Weak transcription	Fetal Brain Female	brain
29	chr1:228884400-228886800	Weak transcription	Placenta	Placenta
30	chr1:228884800-228887600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:228886600-228886800	Enhancers	Gastric	stomach
32	chr1:228886600-228887400	Enhancers	Fetal Thymus	thymus

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