Variant report

Variant	rs7632501
Chromosome Location	chr3:47268306-47268307
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	chr3:47266423..47269047-chr3:47271285..47273402,2	K562	blood:

Extended variants
information (count: 102 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1038394	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs10490798	0.90[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap]
rs1076394	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap]
rs10865946	0.88[CEU][hapmap]
rs11130115	0.82[CEU][hapmap];0.91[TSI][hapmap]
rs11130123	0.89[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs11130124	0.92[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs11130126	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11705957	0.88[CEU][hapmap];0.89[TSI][hapmap]
rs11710013	0.92[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs11710121	0.92[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap]
rs11710322	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap]
rs11711824	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs11712445	0.91[CEU][hapmap]
rs11714373	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11719738	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11719877	0.88[CEU][hapmap];0.87[TSI][hapmap]
rs11915074	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11920354	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11920853	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11921117	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11925560	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12493425	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12631730	0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap]
rs12636851	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs12715421	0.86[AFR][1000 genomes]
rs13061071	0.82[CEU][hapmap];0.91[TSI][hapmap]
rs13075233	0.88[CEU][hapmap];0.87[TSI][hapmap]
rs13094438	0.92[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs1466740	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1466741	0.83[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1531875	0.88[CEU][hapmap];0.87[TSI][hapmap]
rs1638676	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs17410853	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs17411375	0.92[CEU][hapmap];0.93[TSI][hapmap]
rs1811652	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1872164	0.88[CEU][hapmap];0.89[TSI][hapmap]
rs2088135	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2132173	0.81[CEU][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs2159400	0.92[CEU][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap]
rs2240796	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2276853	0.92[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs2276854	0.92[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs295428	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs295441	0.92[CEU][hapmap]
rs295442	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs295449	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs295458	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs295461	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs3736177	0.87[CEU][hapmap]
rs4018905	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4078466	0.89[TSI][hapmap]
rs4082155	0.89[TSI][hapmap]
rs4682852	0.82[CEU][hapmap]
rs4683322	0.92[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4683324	0.83[EUR][1000 genomes]
rs4683326	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs4858824	0.88[CEU][hapmap]
rs4858868	0.88[CEU][hapmap];0.87[TSI][hapmap]
rs56250009	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57756484	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58956475	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62246451	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62246455	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62248905	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6414435	0.84[AFR][1000 genomes]
rs6414436	0.82[AFR][1000 genomes]
rs6442055	0.86[AFR][1000 genomes]
rs6442059	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6766230	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6767907	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6768221	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6772670	0.91[CEU][hapmap]
rs6773521	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6777145	0.83[AFR][1000 genomes]
rs6780013	0.96[CEU][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs6781941	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6791062	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6791842	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs73069104	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7433300	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs7620997	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7636423	0.80[EUR][1000 genomes]
rs807932	0.88[CEU][hapmap];0.91[TSI][hapmap]
rs807936	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs811115	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs922957	0.88[CEU][hapmap]
rs9311403	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9812878	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9818382	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9821119	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9837343	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9844122	0.86[AFR][1000 genomes]
rs9845728	0.88[AFR][1000 genomes]
rs9854790	0.88[AFR][1000 genomes]
rs9858443	0.86[AFR][1000 genomes]
rs9875235	0.83[AFR][1000 genomes]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7632501	DHX30	cis	multi-tissue	Pritchard
rs7632501	C3orf75	cis	cerebellum	SCAN
rs7632501	HYAL2	cis	cerebellum	SCAN
rs7632501	NCKIPSD	cis	cerebellum	SCAN
rs7632501	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs7632501	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs7632501	PRKAR2A	cis	cerebellum	SCAN
rs7632501	SCAP	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47208200-47276600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:47223800-47269200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:47247000-47269400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:47262800-47287400	Weak transcription	Primary T cells from cord blood	blood
5	chr3:47263000-47275600	Weak transcription	HSMMtube	muscle
6	chr3:47263600-47276600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:47264200-47322200	Weak transcription	Gastric	stomach
8	chr3:47265800-47283800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:47266200-47270000	Enhancers	Primary B cells from cord blood	blood
10	chr3:47266200-47270200	Enhancers	Adipose Nuclei	Adipose
11	chr3:47266400-47268400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr3:47266600-47268800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:47266600-47269200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:47266600-47269200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:47266600-47270400	Enhancers	Primary B cells from peripheral blood	blood
16	chr3:47266800-47276400	Weak transcription	Fetal Intestine Small	intestine
17	chr3:47267000-47270400	Weak transcription	Brain Germinal Matrix	brain
18	chr3:47267000-47280400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:47267200-47269200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:47267200-47271000	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr3:47267200-47308000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:47267400-47269800	Enhancers	Liver	Liver
23	chr3:47267400-47281400	Weak transcription	Fetal Stomach	stomach
24	chr3:47267400-47284600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:47267400-47287200	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:47267600-47268600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr3:47267600-47269200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:47267600-47269200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:47267800-47268800	Weak transcription	Placenta	Placenta
30	chr3:47268000-47268400	Enhancers	Brain Cingulate Gyrus	brain
31	chr3:47268000-47269200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:47268000-47269800	Genic enhancers	Fetal Muscle Leg	muscle
33	chr3:47268000-47270200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:47268200-47268400	Flanking Active TSS	GM12878-XiMat	blood
35	chr3:47268200-47270000	Enhancers	Spleen	Spleen

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