Variant report

Variant	rs629120
Chromosome Location	chr3:99425767-99425768
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:99425721-99426752	ProgFib	skin:	n/a	n/a
2	POLR2A	chr3:99424750-99426615	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
COL8A1	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1021102	0.88[YRI][hapmap]
rs1021103	1.00[YRI][hapmap]
rs1038294	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs1087198	0.80[YRI][hapmap]
rs1606481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1607993	0.92[CHD][hapmap];0.92[JPT][hapmap]
rs1630555	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1688771	1.00[YRI][hapmap]
rs1711557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1857290	0.93[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs506186	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs598174	0.92[CHD][hapmap];0.92[JPT][hapmap]
rs651511	0.92[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs668668	0.93[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs694429	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs704570	0.93[CHB][hapmap];0.80[YRI][hapmap]
rs704573	0.93[CHB][hapmap]
rs704582	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs7636447	0.89[YRI][hapmap]
rs792828	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs792829	0.93[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs792834	0.93[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs793445	0.89[YRI][hapmap]
rs793460	0.89[YRI][hapmap]
rs793461	0.89[YRI][hapmap]
rs793462	0.89[YRI][hapmap]
rs793463	0.89[YRI][hapmap]
rs793466	0.89[YRI][hapmap]
rs793467	0.80[YRI][hapmap]
rs793492	0.80[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs793494	0.80[YRI][hapmap]
rs793495	0.80[YRI][hapmap]
rs793496	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs793499	0.84[ASW][hapmap];0.80[CEU][hapmap];1.00[YRI][hapmap]
rs796977	0.80[YRI][hapmap]
rs809415	0.89[YRI][hapmap]
rs812657	0.89[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877217	chr3:99418950-99496351	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs629120	OR5H6	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99394000-99426600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:99397600-99432000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:99411400-99439600	Weak transcription	NHEK	skin
4	chr3:99411800-99426000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:99419000-99428200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:99419800-99430400	Weak transcription	Left Ventricle	heart
7	chr3:99420000-99427000	Weak transcription	Right Atrium	heart
8	chr3:99420000-99428800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:99420000-99429400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:99420000-99432800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:99420000-99433000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:99420600-99430400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:99421000-99427200	Strong transcription	HUVEC	blood vessel
14	chr3:99422200-99426000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:99422400-99425800	Weak transcription	NHLF	lung
16	chr3:99422400-99426200	Strong transcription	HSMM	muscle
17	chr3:99422400-99426200	Weak transcription	HSMMtube	muscle
18	chr3:99422600-99426000	Weak transcription	NH-A	brain
19	chr3:99422600-99431200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr3:99423400-99432400	Genic enhancers	Osteobl	bone
21	chr3:99423800-99440000	Weak transcription	Adipose Nuclei	Adipose
22	chr3:99424000-99426000	Weak transcription	Aorta	Aorta
23	chr3:99424400-99426000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:99424400-99426800	Weak transcription	NHDF-Ad	bronchial
25	chr3:99425000-99428200	Enhancers	Ovary	ovary
26	chr3:99425200-99426000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:99425400-99427000	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr3:99425600-99433000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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