Variant report

Variant	rs346469
Chromosome Location	chr4:86889927-86889928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:86717573..86718676-chr4:86889897..86890637,3	MCF-7	breast:
2	chr4:86717537..86719169-chr4:86889518..86891294,13	MCF-7	breast:

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

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

rs_ID	r²[population]
rs189395	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs189396	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2043647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2136782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2164538	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2575681	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2575682	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2589505	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2589510	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2665869	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2665876	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346470	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346472	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs346473	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs346476	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs346477	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs346482	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]
rs346483	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs346486	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346487	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346489	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346490	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346491	0.91[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346494	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs346496	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs346499	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs346500	0.90[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs346501	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62305515	0.86[ASN][1000 genomes]
rs62305516	0.86[ASN][1000 genomes]
rs62305518	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[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
rs346469	THAP9	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86854000-86893000	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr4:86854200-86893000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr4:86854200-86915800	Weak transcription	Left Ventricle	heart
4	chr4:86863600-86902000	Weak transcription	Pancreas	Pancrea
5	chr4:86875000-86891200	Weak transcription	Right Atrium	heart
6	chr4:86875200-86890800	Weak transcription	Stomach Mucosa	stomach
7	chr4:86875200-86915800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr4:86878000-86893200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr4:86880600-86915800	Weak transcription	Gastric	stomach
10	chr4:86882000-86892000	Enhancers	NHDF-Ad	bronchial
11	chr4:86885000-86915600	Weak transcription	Fetal Lung	lung
12	chr4:86885600-86891800	Enhancers	HUVEC	blood vessel
13	chr4:86886800-86893000	Weak transcription	Primary B cells from cord blood	blood
14	chr4:86887000-86893200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:86887400-86892000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:86887600-86891200	Weak transcription	Spleen	Spleen
17	chr4:86887600-86893000	Weak transcription	Fetal Muscle Leg	muscle
18	chr4:86887600-86915600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr4:86888200-86892400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:86888200-86899200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr4:86888600-86892000	Enhancers	HSMM	muscle
22	chr4:86888800-86919200	Weak transcription	Colon Smooth Muscle	Colon
23	chr4:86889000-86892000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:86889000-86892200	Enhancers	Osteobl	bone
25	chr4:86889200-86890400	Enhancers	NHLF	lung
26	chr4:86889200-86891000	Enhancers	NH-A	brain
27	chr4:86889200-86891200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr4:86889200-86891400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr4:86889200-86893400	Weak transcription	Ovary	ovary
30	chr4:86889400-86915800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr4:86889400-86935000	Weak transcription	Psoas Muscle	Psoas
32	chr4:86889600-86890000	Weak transcription	Fetal Kidney	kidney
33	chr4:86889600-86890600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:86889600-86890800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:86889600-86891200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr4:86889600-86891200	Weak transcription	Adipose Nuclei	Adipose
37	chr4:86889600-86891200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr4:86889600-86891600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr4:86889600-86892000	Enhancers	Muscle Satellite Cultured Cells	--
40	chr4:86889600-86893200	Weak transcription	Primary B cells from peripheral blood	blood
41	chr4:86889600-86904000	Weak transcription	Aorta	Aorta
42	chr4:86889800-86890200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:86889800-86890800	Weak transcription	HSMMtube	muscle
44	chr4:86889800-86892400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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