Variant report

Variant	rs6792461
Chromosome Location	chr3:47473168-47473169
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47468827..47471837-chr3:47472368..47475711,3	K562	blood:
2	chr3:47465811..47468194-chr3:47471734..47473557,2	K562	blood:
3	chr3:47471759..47474582-chr3:47484532..47486796,2	K562	blood:
4	chr3:47468490..47471294-chr3:47472368..47475711,5	K562	blood:
5	chr3:47471198..47476124-chr3:47477779..47481546,5	K562	blood:
6	chr3:47471759..47475390-chr3:47483723..47486796,3	K562	blood:

Variant related genes	Relation type
ENSG00000114650	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1038394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1076394	0.96[CEU][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs10865946	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130123	0.92[CEU][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap]
rs11130124	0.96[CEU][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs11130126	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs11130127	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11130128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130129	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130132	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11130133	0.81[EUR][1000 genomes]
rs11130137	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap]
rs11705957	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11710013	0.96[CEU][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs11710121	0.88[CEU][hapmap]
rs11710322	0.96[CEU][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs11711265	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs11711824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11712445	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11716763	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11719877	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11914913	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11914932	0.82[EUR][1000 genomes]
rs11915074	0.88[CEU][hapmap]
rs11920853	0.88[CEU][hapmap]
rs11925823	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11927371	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12486969	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12487736	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12489046	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12490058	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12492433	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12495169	0.82[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs12497225	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12630641	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12632132	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12636851	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13059519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13064843	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13075233	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13079098	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13094438	0.96[CEU][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap]
rs1531875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1638676	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs17080872	0.83[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs17410853	0.88[CEU][hapmap]
rs17411375	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17784882	0.86[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes]
rs1872164	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1872166	0.91[YRI][hapmap]
rs2062278	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2101247	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2159400	0.96[CEU][hapmap];0.93[GIH][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2276853	0.96[CEU][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs2276854	0.96[CEU][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs2291298	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs295428	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs295441	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs295442	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs295449	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs295458	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs295461	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs3736177	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3816779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4241548	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4683326	0.96[CEU][hapmap]
rs4858805	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4858811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4858824	1.00[CEU][hapmap]
rs4858848	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4858868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4858888	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4858890	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4858893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4858894	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs553989	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56032309	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56351005	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57346147	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59586735	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60369822	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62246474	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62248580	0.87[EUR][1000 genomes]
rs62248599	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62248603	0.83[EUR][1000 genomes]
rs62248605	0.81[EUR][1000 genomes]
rs62260710	0.80[EUR][1000 genomes]
rs62260711	0.80[EUR][1000 genomes]
rs6765990	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6768221	0.88[CEU][hapmap]
rs6780013	0.86[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs6787422	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6791842	0.96[CEU][hapmap]
rs6792488	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6800271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73081205	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7613282	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7628631	0.82[EUR][1000 genomes]
rs7641010	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7649234	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7651194	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7651762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs807810	0.88[EUR][1000 genomes]
rs807931	0.86[EUR][1000 genomes]
rs807932	0.92[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs807936	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs811115	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs8180040	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs878659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs922957	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9683033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9683177	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6792461	C3orf75	cis	cerebellum	SCAN
rs6792461	RTP3	cis	lesional skin	skin_eQTL
rs6792461	IFRD2	cis	parietal	SCAN
rs6792461	HYAL2	cis	cerebellum	SCAN
rs6792461	SCAP	cis	parietal	SCAN
rs6792461	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs6792461	PRKAR2A	cis	cerebellum	SCAN
rs6792461	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs6792461	CCDC12	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47441000-47476800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:47450400-47484800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:47461800-47478800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr3:47463000-47485200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:47463200-47474400	Weak transcription	Fetal Kidney	kidney
6	chr3:47463400-47475400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:47463400-47477600	Strong transcription	Fetal Thymus	thymus
8	chr3:47463400-47484600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:47463600-47476800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:47463600-47476800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:47463600-47484800	Strong transcription	Primary T cells from cord blood	blood
12	chr3:47463800-47476800	Strong transcription	Fetal Muscle Leg	muscle
13	chr3:47463800-47479400	Weak transcription	A549	lung
14	chr3:47464000-47474800	Weak transcription	HSMM	muscle
15	chr3:47464000-47476600	Strong transcription	Stomach Smooth Muscle	stomach
16	chr3:47464000-47476800	Strong transcription	Dnd41	blood
17	chr3:47464000-47484200	Weak transcription	Right Atrium	heart
18	chr3:47464600-47473200	Strong transcription	Primary B cells from cord blood	blood
19	chr3:47464600-47474000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:47464600-47476800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:47464600-47476800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:47464800-47476600	Strong transcription	Spleen	Spleen
23	chr3:47464800-47477200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr3:47465200-47476600	Strong transcription	Lung	lung
25	chr3:47465200-47476800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:47465200-47476800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr3:47465200-47476800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr3:47465200-47476800	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr3:47465400-47473200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:47465400-47484600	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr3:47465600-47476800	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:47465600-47476800	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr3:47465600-47476800	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr3:47465600-47484200	Strong transcription	Primary B cells from peripheral blood	blood
35	chr3:47466200-47475200	Weak transcription	Small Intestine	intestine
36	chr3:47467000-47474400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr3:47467000-47474600	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr3:47467600-47474400	Weak transcription	NHLF	lung
39	chr3:47467800-47474400	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr3:47467800-47474800	Weak transcription	Psoas Muscle	Psoas
41	chr3:47467800-47475400	Strong transcription	Duodenum Mucosa	Duodenum
42	chr3:47469200-47484400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr3:47469800-47474600	Weak transcription	Fetal Lung	lung
44	chr3:47470000-47474400	Weak transcription	HSMMtube	muscle
45	chr3:47470000-47481200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr3:47470200-47474000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:47470200-47474000	Weak transcription	Aorta	Aorta
48	chr3:47470200-47474200	Weak transcription	Ovary	ovary
49	chr3:47470400-47474000	Weak transcription	Brain Germinal Matrix	brain
50	chr3:47470800-47475800	Strong transcription	K562	blood

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