Variant report

Variant	rs8180040
Chromosome Location	chr3:47388947-47388948
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47374984..47378257-chr3:47387445..47390944,5	K562	blood:
2	chr3:47374984..47381273-chr3:47386586..47390760,8	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHL18-2	chr3:47388823-47390563	NONHSAT089495

Extended variants
information (count: 90 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1038394	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs1076394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs10865946	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs11130123	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs11130124	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs11130126	0.92[CEU][hapmap];0.93[TSI][hapmap]
rs11130127	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11130128	0.96[CEU][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes]
rs11130129	0.96[CEU][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes]
rs11130137	0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs11705957	0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11710013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs11710121	0.85[CEU][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap]
rs11710322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs11711265	0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs11711824	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs11712445	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs11716763	0.96[CEU][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs11719877	0.96[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs11915074	0.92[CEU][hapmap]
rs11920853	0.92[CEU][hapmap]
rs11925823	0.86[EUR][1000 genomes]
rs11927371	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12486969	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12487736	0.81[EUR][1000 genomes]
rs12495169	0.85[JPT][hapmap]
rs12497225	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12636851	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.80[LWK][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13059519	0.96[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs13064843	0.86[EUR][1000 genomes]
rs13075233	0.96[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs13079098	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13094438	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs1531875	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs1638676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs17080872	0.81[JPT][hapmap]
rs17410853	1.00[ASW][hapmap];0.85[CEU][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17411375	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17784882	0.85[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.88[LWK][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap]
rs1872164	0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2062278	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2101247	0.92[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.80[LWK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes]
rs2132173	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap]
rs2159400	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276853	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs2276854	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]
rs2291298	0.96[CEU][hapmap]
rs295428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs295442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs295449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs295458	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3736177	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3816779	0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs4683326	1.00[CEU][hapmap]
rs4858805	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4858811	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs4858824	0.96[CEU][hapmap]
rs4858848	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4858868	0.96[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs4858888	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858890	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858893	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs4858894	0.87[CEU][hapmap];0.88[JPT][hapmap]
rs553989	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56032309	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56351005	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57346147	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60369822	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62246474	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6768221	0.92[CEU][hapmap]
rs6772670	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs6780013	0.85[ASW][hapmap];0.89[CEU][hapmap];0.89[TSI][hapmap]
rs6787422	0.86[EUR][1000 genomes]
rs6791842	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs6792461	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6800271	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7613282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641010	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7651762	0.96[CEU][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs807810	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs807931	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs807932	0.96[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]
rs807936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs811115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs878659	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs922957	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9683033	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]

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

Variant related diseases (count:1)

Disease	PMID	Source
Colorectal cancer	23350875	GWAS catalog

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs8180040	RTP3	cis	lesional skin	skin_eQTL
rs8180040	AMIGO3	cis	cerebellum	SCAN
rs8180040	C3orf75	cis	cerebellum	SCAN
rs8180040	HYAL2	cis	cerebellum	SCAN
rs8180040	PRKAR2A	cis	cerebellum	SCAN
rs8180040	SCAP	cis	parietal	SCAN
rs8180040	CCDC12	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47361400-47389800	Weak transcription	Right Atrium	heart
2	chr3:47372000-47389200	Weak transcription	Psoas Muscle	Psoas
3	chr3:47376600-47389400	Weak transcription	Fetal Lung	lung
4	chr3:47379800-47389200	Weak transcription	Hela-S3	cervix
5	chr3:47381800-47389600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:47382200-47389200	Weak transcription	Fetal Kidney	kidney
7	chr3:47383200-47389000	Weak transcription	Fetal Brain Male	brain
8	chr3:47386200-47389000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:47386200-47395600	Weak transcription	Ovary	ovary
10	chr3:47386400-47389600	Enhancers	Primary hematopoietic stem cells	blood
11	chr3:47386800-47389200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:47386800-47389200	Weak transcription	Aorta	Aorta
13	chr3:47386800-47390400	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr3:47386800-47400800	Weak transcription	Pancreas	Pancrea
15	chr3:47387000-47389200	Weak transcription	HepG2	liver
16	chr3:47387000-47389400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:47387000-47389400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:47387000-47390200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr3:47387000-47390400	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:47387000-47390400	Weak transcription	Gastric	stomach
21	chr3:47387000-47390600	Weak transcription	Thymus	Thymus
22	chr3:47387200-47389400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr3:47387400-47389000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr3:47387400-47389600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr3:47387400-47389600	Weak transcription	Liver	Liver
26	chr3:47387600-47389000	Enhancers	Primary B cells from cord blood	blood
27	chr3:47387600-47389200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:47387600-47390400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:47387600-47397200	Weak transcription	Lung	lung
30	chr3:47387800-47389400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:47387800-47389400	Weak transcription	Dnd41	blood
32	chr3:47387800-47389400	Enhancers	NHDF-Ad	bronchial
33	chr3:47387800-47389600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:47387800-47389600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr3:47387800-47389600	Enhancers	HSMMtube	muscle
36	chr3:47388000-47389000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:47388000-47389000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:47388000-47389200	Weak transcription	Esophagus	oesophagus
39	chr3:47388000-47389200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr3:47388000-47389400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:47388000-47389400	Enhancers	HSMM	muscle
42	chr3:47388000-47389600	Weak transcription	Brain Angular Gyrus	brain
43	chr3:47388000-47389600	Enhancers	NHLF	lung
44	chr3:47388000-47389800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:47388000-47389800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:47388000-47389800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:47388000-47389800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:47388000-47389800	Enhancers	Primary B cells from peripheral blood	blood
49	chr3:47388000-47390200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:47388000-47390600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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