Variant report

Variant	rs2276854
Chromosome Location	chr3:47276968-47276969
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47276902..47279384-chr3:47323090..47325567,2	K562	blood:
2	chr3:47276373..47278773-chr3:47281395..47283848,2	K562	blood:
3	chr3:47276538..47278116-chr3:47285524..47288270,2	K562	blood:

Variant related genes	Relation type
ENSG00000114648	Chromatin interaction
ENSG00000088727	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1038394	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs1076394	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10865946	0.96[CEU][hapmap]
rs11130114	0.84[ASN][1000 genomes]
rs11130115	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.85[ASN][1000 genomes]
rs11130123	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11130124	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130126	0.92[CEU][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs11705957	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs11708451	0.86[ASN][1000 genomes]
rs11710013	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11710121	0.85[CEU][hapmap]
rs11710322	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11711824	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs11712445	0.96[CEU][hapmap]
rs11712716	0.85[ASN][1000 genomes]
rs11714294	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11716539	0.85[ASN][1000 genomes]
rs11718795	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11719306	0.82[ASN][1000 genomes]
rs11719877	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs11915074	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs11920354	0.87[EUR][1000 genomes]
rs11920853	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs11921117	0.81[EUR][1000 genomes]
rs11925560	0.86[EUR][1000 genomes]
rs12488225	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12489211	0.87[ASN][1000 genomes]
rs12629262	0.83[ASN][1000 genomes]
rs12635619	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12636851	0.96[CEU][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs13061071	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.83[ASN][1000 genomes]
rs13062022	0.85[ASN][1000 genomes]
rs13063250	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13075233	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs13078131	0.81[ASN][1000 genomes]
rs13084117	0.85[ASN][1000 genomes]
rs13094438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094672	0.84[ASN][1000 genomes]
rs13098228	0.83[ASN][1000 genomes]
rs1531875	0.96[CEU][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs1638676	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17410853	0.85[CEU][hapmap]
rs17411375	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs17476234	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1872164	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs2088135	0.90[EUR][1000 genomes]
rs2132173	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2159400	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs2276853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295428	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs295441	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs295442	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs295449	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap]
rs295458	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs295461	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs3736177	0.96[CEU][hapmap]
rs4078466	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap]
rs4082155	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs4682852	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.85[ASN][1000 genomes]
rs4683320	0.84[ASN][1000 genomes]
rs4683322	0.81[CEU][hapmap];0.89[TSI][hapmap]
rs4683324	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4683326	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4858824	0.96[CEU][hapmap]
rs4858868	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs56250009	0.90[EUR][1000 genomes]
rs62248905	0.89[EUR][1000 genomes]
rs6767907	0.81[CEU][hapmap];0.91[TSI][hapmap]
rs6768221	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs6772670	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6780013	0.89[CEU][hapmap];0.84[TSI][hapmap]
rs6785790	0.84[ASN][1000 genomes]
rs6791842	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6792461	0.96[CEU][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs6800271	0.83[ASW][hapmap];0.96[CEU][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap]
rs73069104	0.81[EUR][1000 genomes]
rs7615323	0.85[ASN][1000 genomes]
rs7621911	0.80[ASN][1000 genomes]
rs7632501	0.88[EUR][1000 genomes]
rs7636423	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7651762	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs807932	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs807935	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs807936	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs807937	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs811115	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs922957	0.96[CEU][hapmap]
rs9311403	0.84[CEU][hapmap]
rs9837343	0.81[CEU][hapmap];0.91[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1014457	chr3:47222292-47335175	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv536560	chr3:47222292-47335175	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	esv1799921	chr3:47259253-47283105	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2276854	RTP3	cis	lesional skin	skin_eQTL
rs2276854	PRKAR2A	cis	cerebellum	SCAN
rs2276854	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs2276854	CCHCR1	trans	lymphoblastoid	seeQTL
rs2276854	SCAP	cis	parietal	SCAN
rs2276854	HYAL2	cis	cerebellum	SCAN
rs2276854	AMIGO3	cis	cerebellum	SCAN
rs2276854	CCDC12	cis	cerebellum	SCAN
rs2276854	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs2276854	C3orf75	cis	cerebellum	SCAN
rs2276854	NCKIPSD	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47262800-47287400	Weak transcription	Primary T cells from cord blood	blood
2	chr3:47264200-47322200	Weak transcription	Gastric	stomach
3	chr3:47265800-47283800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:47267000-47280400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:47267200-47308000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:47267400-47281400	Weak transcription	Fetal Stomach	stomach
7	chr3:47267400-47284600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:47267400-47287200	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:47269800-47281000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:47269800-47281200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:47269800-47288400	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:47270000-47277800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:47270000-47284600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:47270200-47288600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:47270600-47286800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:47270800-47307800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:47271200-47281000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:47271400-47308000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:47272600-47288200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:47273600-47277000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr3:47275800-47277000	Enhancers	Liver	Liver
22	chr3:47275800-47277000	Enhancers	Fetal Intestine Large	intestine
23	chr3:47275800-47277600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:47276200-47283000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:47276400-47277000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:47276400-47277000	Enhancers	NH-A	brain
27	chr3:47276400-47277400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:47276400-47277600	ZNF genes & repeats	Lung	lung
29	chr3:47276400-47305200	Weak transcription	Brain Anterior Caudate	brain
30	chr3:47276600-47277000	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr3:47276600-47277000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr3:47276600-47277000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:47276600-47277400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:47276600-47277400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:47276600-47277600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:47276600-47283800	Weak transcription	Right Ventricle	heart
37	chr3:47276800-47277000	Enhancers	Placenta Amnion	Placenta Amnion
38	chr3:47276800-47277200	Enhancers	HepG2	liver
39	chr3:47276800-47281400	Weak transcription	Fetal Intestine Small	intestine
40	chr3:47276800-47284000	Weak transcription	HSMMtube	muscle
41	chr3:47276800-47284600	Weak transcription	Pancreas	Pancrea
42	chr3:47276800-47285200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:47276800-47285200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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