Variant report

Variant	rs4352239
Chromosome Location	chr2:113083283-113083284
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10167748	0.96[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[JPT][hapmap];1.00[ASN][1000 genomes]
rs10203614	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10203843	0.96[ASN][1000 genomes]
rs10205038	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10205897	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10211300	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs10439391	0.96[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];0.96[ASN][1000 genomes]
rs10864903	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11123132	0.94[CHB][hapmap];1.00[YRI][hapmap]
rs11123135	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11123136	0.93[ASN][1000 genomes]
rs11674953	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11691431	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11896500	0.94[ASN][1000 genomes]
rs11903741	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11904424	0.91[ASN][1000 genomes]
rs12464478	0.85[ASN][1000 genomes]
rs12464895	1.00[YRI][hapmap]
rs12711738	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12711739	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13387611	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs34471791	0.86[ASN][1000 genomes]
rs4258804	0.96[ASN][1000 genomes]
rs4299347	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]
rs4332934	0.96[ASN][1000 genomes]
rs4392265	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4399734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4419238	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4430968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4446076	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4450606	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4450607	0.95[ASN][1000 genomes]
rs4456711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4507112	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4522611	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4525706	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4539797	0.96[ASN][1000 genomes]
rs4542853	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4578863	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];1.00[ASN][1000 genomes]
rs4622729	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4630773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849058	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58337061	0.96[ASN][1000 genomes]
rs62160223	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6542045	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6542051	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6542052	0.91[ASN][1000 genomes]
rs6542053	1.00[ASN][1000 genomes]
rs6542054	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706874	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs6708164	0.97[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];0.96[ASN][1000 genomes]
rs6726412	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6733138	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6744364	0.98[ASN][1000 genomes]
rs6751146	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6758110	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6761599	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs71414636	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7557281	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7557862	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7564052	0.96[ASN][1000 genomes]
rs7569894	1.00[ASN][1000 genomes]
rs7571435	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7579561	0.98[ASN][1000 genomes]
rs7591439	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7598168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7599041	0.96[ASN][1000 genomes]
rs7600338	0.96[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];0.96[ASN][1000 genomes]
rs7601200	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601888	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8179708	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv874869	chr2:113021811-113089267	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv874870	chr2:113021811-113097699	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	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
9	nsv874873	chr2:113027569-113083367	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv874874	chr2:113027569-113089267	Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
11	nsv874876	chr2:113051291-113089267	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4352239	RGPD8	cis	lung	GTEx
rs4352239	RGPD8	cis	Artery Tibial	GTEx
rs4352239	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs4352239	RGPD8	cis	Muscle Skeletal	GTEx
rs4352239	RGPD8	cis	Nerve Tibial	GTEx
rs4352239	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113034400-113097000	Weak transcription	Psoas Muscle	Psoas
2	chr2:113048000-113084400	Weak transcription	Fetal Kidney	kidney
3	chr2:113050600-113090600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:113051000-113088600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:113051600-113088600	Weak transcription	Esophagus	oesophagus
6	chr2:113053400-113085400	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:113056400-113089000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr2:113057000-113099400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:113058200-113090600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr2:113058800-113088800	Weak transcription	Dnd41	blood
11	chr2:113059000-113088800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:113059200-113096800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:113059600-113090000	Weak transcription	Colonic Mucosa	Colon
14	chr2:113060000-113084800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:113060000-113090600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:113060400-113090600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:113061600-113088800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:113062200-113084000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr2:113062200-113094400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:113062400-113088800	Weak transcription	Aorta	Aorta
21	chr2:113062400-113090600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr2:113068200-113101400	Weak transcription	NHDF-Ad	bronchial
23	chr2:113068400-113087000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:113068800-113084600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:113069000-113097000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:113069600-113088600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:113070000-113093600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:113070400-113084400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr2:113071000-113087000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:113072400-113089000	Weak transcription	Fetal Heart	heart
31	chr2:113075400-113094400	Weak transcription	NHLF	lung
32	chr2:113076400-113084400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:113079800-113083600	Strong transcription	Fetal Stomach	stomach
34	chr2:113079800-113093200	Weak transcription	HSMM	muscle
35	chr2:113080000-113083400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr2:113080000-113083800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr2:113080000-113085400	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:113080200-113085400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:113080400-113083400	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr2:113080400-113083400	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr2:113080600-113083400	Strong transcription	Brain Hippocampus Middle	brain
42	chr2:113080600-113083400	Strong transcription	Fetal Intestine Large	intestine
43	chr2:113080600-113084400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:113080600-113085800	Strong transcription	Ovary	ovary
45	chr2:113080600-113086000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:113080800-113083800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr2:113080800-113088800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:113081000-113085600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:113081200-113085800	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr2:113081400-113091200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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