Variant report

Variant	rs6768722
Chromosome Location	chr3:47079112-47079113
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47068198..47069925-chr3:47079015..47080516,2	K562	blood:
2	chr3:47072469..47075207-chr3:47077387..47079210,2	K562	blood:

Extended variants
information (count: 118 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10433549	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10461018	0.92[ASW][hapmap];0.88[CEU][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap]
rs1079276	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs1108301	0.81[EUR][1000 genomes]
rs11130110	0.88[CEU][hapmap];0.89[TSI][hapmap]
rs11130111	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs11130112	0.88[CEU][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs11130115	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs11707736	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11709660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11713693	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11714373	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11715121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11719738	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11720139	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11917361	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11917474	0.80[EUR][1000 genomes]
rs11923706	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12493425	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12631730	0.90[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs12715421	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13061071	0.92[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs13062681	0.85[EUR][1000 genomes]
rs13066214	0.82[EUR][1000 genomes]
rs13077398	0.80[EUR][1000 genomes]
rs13091054	0.86[EUR][1000 genomes]
rs13094438	0.80[CEU][hapmap];0.88[TSI][hapmap]
rs13098228	0.81[EUR][1000 genomes]
rs1466740	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1466741	0.95[CEU][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs17784127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1811652	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1869869	0.80[EUR][1000 genomes]
rs2061197	0.83[ASW][hapmap];0.88[CEU][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap]
rs2132173	0.92[CEU][hapmap];0.88[TSI][hapmap]
rs2276854	0.80[CEU][hapmap];0.89[TSI][hapmap]
rs2278963	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2305634	0.92[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs2305635	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2305638	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs2385867	0.85[EUR][1000 genomes]
rs34103310	0.91[EUR][1000 genomes]
rs34344887	0.81[EUR][1000 genomes]
rs4018905	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4078466	0.92[CEU][hapmap];0.80[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs4082155	0.92[CEU][hapmap];0.80[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs4234465	0.88[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs4682831	0.81[EUR][1000 genomes]
rs4682837	0.88[CEU][hapmap]
rs4682844	0.83[ASW][hapmap];0.88[CEU][hapmap];0.88[TSI][hapmap];0.91[YRI][hapmap]
rs4682852	0.92[CEU][hapmap]
rs4683296	0.91[YRI][hapmap]
rs4683297	0.91[YRI][hapmap]
rs4683322	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55724164	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55843455	0.81[EUR][1000 genomes]
rs55927279	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56217494	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56249396	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57756484	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58956475	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61729713	0.81[EUR][1000 genomes]
rs62246375	0.80[EUR][1000 genomes]
rs62246398	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62246402	0.81[AFR][1000 genomes]
rs62246451	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62246455	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6414435	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6414436	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6442055	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6442059	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6442060	0.84[ASN][1000 genomes]
rs66539935	0.81[EUR][1000 genomes]
rs6763236	0.89[EUR][1000 genomes]
rs6766230	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6767218	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6767907	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6772670	0.95[CEU][hapmap]
rs6773521	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6777145	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6781941	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6791062	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6794193	0.87[EUR][1000 genomes]
rs7373821	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7426969	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7433300	0.92[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.80[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs749511	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs749512	0.92[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7610620	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7610636	0.86[EUR][1000 genomes]
rs7620997	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7621911	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7623888	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7625067	0.88[EUR][1000 genomes]
rs7625070	0.88[EUR][1000 genomes]
rs7628747	0.88[CEU][hapmap];0.89[TSI][hapmap]
rs7633435	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7633698	0.80[EUR][1000 genomes]
rs7636252	0.80[EUR][1000 genomes]
rs7637302	0.85[EUR][1000 genomes]
rs7645278	0.91[YRI][hapmap]
rs9311403	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9812878	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9818382	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9821119	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9837343	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9843075	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9844122	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9845728	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9852082	0.86[YRI][hapmap]
rs9854790	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9858443	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875235	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS 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	28 gene(s)	inside rSNPs	diseases
4	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
5	nsv997261	chr3:47054766-47133680	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6768722	SCAP	cis	parietal	SCAN
rs6768722	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs6768722	CCDC12	cis	cerebellum	SCAN
rs6768722	SCAP	cis	cerebellum	SCAN
rs6768722	C3orf75	cis	cerebellum	SCAN
rs6768722	HYAL2	cis	cerebellum	SCAN
rs6768722	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs6768722	PRKAR2A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47061200-47083000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:47069600-47088200	Strong transcription	Liver	Liver
3	chr3:47069600-47088200	Strong transcription	Fetal Intestine Large	intestine
4	chr3:47069600-47089000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:47069800-47086600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:47070200-47080600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:47070400-47089000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:47073400-47087600	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:47073600-47079600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:47073600-47087800	Strong transcription	Fetal Muscle Leg	muscle
11	chr3:47073600-47088200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:47073800-47079600	Strong transcription	Thymus	Thymus
13	chr3:47073800-47082800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:47073800-47083200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:47073800-47088200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:47074000-47080400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:47074000-47081600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:47074200-47080400	Strong transcription	Adipose Nuclei	Adipose
19	chr3:47074200-47086600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:47074200-47086800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:47074400-47079800	Strong transcription	Primary B cells from cord blood	blood
22	chr3:47074400-47088600	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr3:47074600-47079400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:47074600-47079800	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:47074600-47079800	Strong transcription	Left Ventricle	heart
26	chr3:47074600-47080600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:47074600-47084200	Strong transcription	Fetal Muscle Trunk	muscle
28	chr3:47074600-47084400	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr3:47074600-47085400	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:47074600-47086600	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:47074600-47088200	Strong transcription	NH-A	brain
32	chr3:47074600-47088400	Strong transcription	Placenta	Placenta
33	chr3:47074800-47079400	Strong transcription	Spleen	Spleen
34	chr3:47074800-47079800	Strong transcription	HUVEC	blood vessel
35	chr3:47074800-47088800	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr3:47075400-47079800	Strong transcription	Aorta	Aorta
37	chr3:47075400-47079800	Strong transcription	A549	lung
38	chr3:47075400-47079800	Strong transcription	NHEK	skin
39	chr3:47075400-47079800	Strong transcription	NHLF	lung
40	chr3:47075400-47088200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr3:47075600-47079800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:47075600-47079800	Strong transcription	HSMM	muscle
43	chr3:47075600-47088200	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:47075800-47079600	Strong transcription	Lung	lung
45	chr3:47075800-47079800	Strong transcription	Osteobl	bone
46	chr3:47075800-47085000	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:47075800-47086600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:47076000-47079400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:47076000-47079400	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr3:47076000-47079600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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