Variant report

Variant	rs4299347
Chromosome Location	chr2:113098812-113098813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10167748	0.94[ASN][1000 genomes]
rs10175234	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10177573	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10183121	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs10191002	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10203614	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10203843	0.94[ASN][1000 genomes]
rs10205038	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs10205897	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10211300	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs10439391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10864903	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11123132	0.94[CHB][hapmap];1.00[YRI][hapmap]
rs11123135	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11123136	0.91[ASN][1000 genomes]
rs11674953	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11691431	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11896500	0.92[ASN][1000 genomes]
rs11903741	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11904424	0.89[ASN][1000 genomes]
rs12464478	0.85[ASN][1000 genomes]
rs12464895	1.00[YRI][hapmap]
rs12711738	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs12711739	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13387611	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34471791	0.85[ASN][1000 genomes]
rs4258804	0.94[ASN][1000 genomes]
rs4332934	0.94[ASN][1000 genomes]
rs4352239	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4392265	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4399734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4419238	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4430968	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4446076	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4450606	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4450607	0.93[ASN][1000 genomes]
rs4456711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4507112	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4522611	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4525706	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4539797	0.94[ASN][1000 genomes]
rs4542853	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4578863	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4622729	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4630773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849058	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58337061	0.94[ASN][1000 genomes]
rs62160223	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6542045	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs6542051	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6542052	0.89[ASN][1000 genomes]
rs6542053	0.98[ASN][1000 genomes]
rs6542054	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6706874	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs6708164	0.95[ASN][1000 genomes]
rs6716010	0.85[EUR][1000 genomes]
rs6725933	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6726412	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6733138	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6744364	1.00[ASN][1000 genomes]
rs6751146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6758110	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6761599	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs71414636	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7557281	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7557862	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7564052	0.94[ASN][1000 genomes]
rs7569894	0.98[ASN][1000 genomes]
rs7571435	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7579561	1.00[ASN][1000 genomes]
rs7591439	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7598168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7599041	0.98[ASN][1000 genomes]
rs7600338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7601200	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7601888	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8179708	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv582703	chr2:112920219-113100014	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv874871	chr2:113021811-113217630	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4299347	RGPD8	cis	Nerve Tibial	GTEx
rs4299347	RGPD8	cis	Muscle Skeletal	GTEx
rs4299347	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs4299347	FBLN7	cis	parietal	SCAN
rs4299347	POLR1B	cis	parietal	SCAN
rs4299347	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs4299347	RGPD8	cis	Artery Tibial	GTEx
rs4299347	RGPD8	cis	lung	GTEx
rs4299347	TMEM87B	cis	parietal	SCAN
rs4299347	POLR1B	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113057000-113099400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr2:113068200-113101400	Weak transcription	NHDF-Ad	bronchial
3	chr2:113085800-113103600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:113089400-113103400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:113089600-113100600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:113089600-113101400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:113089600-113101400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:113089800-113101000	Weak transcription	Adipose Nuclei	Adipose
9	chr2:113090000-113101000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:113090000-113101200	Weak transcription	Fetal Muscle Leg	muscle
11	chr2:113090000-113101600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:113090000-113103400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:113090000-113103400	Weak transcription	Spleen	Spleen
14	chr2:113095400-113100800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr2:113096800-113101400	Enhancers	Fetal Intestine Large	intestine
16	chr2:113097000-113099600	Enhancers	Fetal Intestine Small	intestine
17	chr2:113097000-113100200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:113097400-113101600	Weak transcription	HepG2	liver
19	chr2:113097800-113100200	Enhancers	NHEK	skin
20	chr2:113098200-113100200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:113098400-113104400	Weak transcription	Fetal Kidney	kidney
22	chr2:113098600-113099400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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