Variant report

Variant	rs346482
Chromosome Location	chr4:86876674-86876675
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs189395	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs189396	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2043647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2136782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2164538	1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2575681	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2575682	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2589505	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2589510	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2665869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2665876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346470	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346472	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346473	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346476	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs346477	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346483	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346486	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346487	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346489	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346490	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346491	0.91[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346494	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346496	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346499	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs346500	0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs346501	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62305515	0.89[ASN][1000 genomes]
rs62305516	0.89[ASN][1000 genomes]
rs62305518	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][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	nsv830000	chr4:86745341-86909059	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv879520	chr4:86829529-86918232	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs346482	THAP9	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86854000-86893000	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr4:86854200-86880200	Weak transcription	Gastric	stomach
3	chr4:86854200-86893000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr4:86854200-86915800	Weak transcription	Left Ventricle	heart
5	chr4:86862400-86877200	Weak transcription	Liver	Liver
6	chr4:86863600-86902000	Weak transcription	Pancreas	Pancrea
7	chr4:86864000-86877000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr4:86875000-86877000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr4:86875000-86887200	Weak transcription	Fetal Stomach	stomach
10	chr4:86875000-86891200	Weak transcription	Right Atrium	heart
11	chr4:86875200-86876800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr4:86875200-86876800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr4:86875200-86877600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:86875200-86877800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:86875200-86886800	Weak transcription	Adipose Nuclei	Adipose
16	chr4:86875200-86889000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:86875200-86889000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:86875200-86890800	Weak transcription	Stomach Mucosa	stomach
19	chr4:86875200-86915800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr4:86875400-86876800	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr4:86875400-86877000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:86875400-86877000	Weak transcription	HMEC	breast
23	chr4:86875400-86883200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:86875400-86888200	Weak transcription	HSMMtube	muscle
25	chr4:86875600-86877000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:86875600-86882200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:86875600-86887400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:86875800-86877200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr4:86875800-86880000	Weak transcription	Fetal Muscle Leg	muscle
30	chr4:86875800-86888600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr4:86875800-86888600	Weak transcription	HSMM	muscle
32	chr4:86876200-86877200	Enhancers	Primary hematopoietic stem cells	blood
33	chr4:86876200-86877800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr4:86876200-86878800	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr4:86876400-86877200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr4:86876400-86877400	Enhancers	Fetal Kidney	kidney
37	chr4:86876400-86877400	Enhancers	K562	blood
38	chr4:86876400-86877600	Strong transcription	Primary B cells from cord blood	blood
39	chr4:86876400-86877600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr4:86876400-86877600	Enhancers	Hela-S3	cervix
41	chr4:86876400-86877600	Strong transcription	HUVEC	blood vessel
42	chr4:86876400-86878600	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr4:86876400-86878800	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr4:86876600-86876800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr4:86876600-86876800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:86876600-86876800	Enhancers	H9 Cell Line	embryonic stem cell
47	chr4:86876600-86876800	Enhancers	A549	lung
48	chr4:86876600-86877000	Enhancers	Stomach Smooth Muscle	stomach
49	chr4:86876600-86877200	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr4:86876600-86877200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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