Variant report

Variant	rs6772670
Chromosome Location	chr3:47191349-47191350
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	chr3:47189860..47191745-chr3:47198153..47199687,2	K562	blood:
2	chr3:47189967..47191564-chr3:47204385..47206673,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227398	Chromatin interaction
ENSG00000181555	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10433549	0.95[CEU][hapmap]
rs10461018	0.95[CEU][hapmap]
rs1076394	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1079276	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs11130110	0.95[CEU][hapmap]
rs11130111	0.96[CEU][hapmap]
rs11130112	0.95[CEU][hapmap]
rs11130114	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130123	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs11130124	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11130126	0.91[CEU][hapmap]
rs11708451	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11710013	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs11710121	0.83[CEU][hapmap]
rs11710322	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs11712716	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714282	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11714373	0.90[EUR][1000 genomes]
rs11716539	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718795	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11719306	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11719738	0.91[EUR][1000 genomes]
rs11720139	0.95[CEU][hapmap]
rs11915074	0.92[CEU][hapmap]
rs11920853	0.92[CEU][hapmap]
rs11923706	0.85[EUR][1000 genomes]
rs12488225	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12489211	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12493425	0.91[EUR][1000 genomes]
rs12629262	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12635619	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13061071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13062022	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13063250	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13078131	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13084117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13091054	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13094438	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs13094672	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13098228	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1466740	0.84[EUR][1000 genomes]
rs1466741	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs1638676	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs17410853	0.83[CEU][hapmap]
rs17784127	0.91[CEU][hapmap]
rs1811652	0.91[EUR][1000 genomes]
rs2061197	0.95[CEU][hapmap]
rs2132173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2159400	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2276853	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2276854	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2278963	0.95[CEU][hapmap]
rs2305634	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2305635	0.95[CEU][hapmap]
rs2305638	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs295428	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs295441	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs295442	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs295449	0.95[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs295458	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs295461	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap]
rs34103310	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4018905	0.88[EUR][1000 genomes]
rs4078466	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4082155	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4234465	0.95[CEU][hapmap]
rs4682837	0.96[CEU][hapmap]
rs4682852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683320	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683322	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs4683324	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683326	0.95[CEU][hapmap]
rs57756484	0.87[EUR][1000 genomes]
rs58956475	0.90[EUR][1000 genomes]
rs62246451	0.91[EUR][1000 genomes]
rs62246455	0.88[EUR][1000 genomes]
rs6414435	0.80[EUR][1000 genomes]
rs6414436	0.84[EUR][1000 genomes]
rs6442055	0.80[EUR][1000 genomes]
rs6442059	0.91[EUR][1000 genomes]
rs6763236	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6766230	0.91[EUR][1000 genomes]
rs6767907	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs6768221	0.91[CEU][hapmap]
rs6773521	0.88[EUR][1000 genomes]
rs6777145	0.80[EUR][1000 genomes]
rs6781941	0.86[EUR][1000 genomes]
rs6785790	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6791062	0.89[EUR][1000 genomes]
rs6791842	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6794193	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7433300	0.81[CEU][hapmap]
rs749511	0.95[CEU][hapmap]
rs749512	0.86[CEU][hapmap]
rs7610636	0.81[EUR][1000 genomes]
rs7615323	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620997	0.81[EUR][1000 genomes]
rs7621911	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7625067	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7625070	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7628747	0.95[CEU][hapmap]
rs807932	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs807936	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs811115	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs9311403	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs9812878	0.81[EUR][1000 genomes]
rs9818382	0.91[EUR][1000 genomes]
rs9821119	0.91[EUR][1000 genomes]
rs9837343	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs9843075	0.87[EUR][1000 genomes]
rs9854790	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv590210	chr3:47126543-47214122	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv590211	chr3:47189485-47256057	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6772670	RTP3	cis	lesional skin	skin_eQTL
rs6772670	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs6772670	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47165800-47197000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:47166000-47200800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:47166000-47201200	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:47166000-47204600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:47166200-47197200	Weak transcription	Aorta	Aorta
6	chr3:47166200-47200600	Weak transcription	Hela-S3	cervix
7	chr3:47166400-47194200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:47166600-47204200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:47167400-47202400	Weak transcription	HSMM	muscle
10	chr3:47167800-47195400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:47175800-47200400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:47177800-47194200	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:47178000-47194200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:47181000-47193600	Weak transcription	Fetal Heart	heart
15	chr3:47182000-47192600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr3:47182000-47195400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:47182600-47200800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:47182800-47192000	Weak transcription	Stomach Mucosa	stomach
19	chr3:47182800-47198200	Weak transcription	Primary B cells from cord blood	blood
20	chr3:47183600-47192000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:47183600-47193800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:47183600-47200800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:47183600-47202200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:47183800-47193800	Weak transcription	Primary T cells from cord blood	blood
25	chr3:47183800-47194000	Weak transcription	Dnd41	blood
26	chr3:47183800-47194200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:47183800-47194400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:47183800-47198000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:47183800-47202200	Weak transcription	NHEK	skin
30	chr3:47183800-47203000	Weak transcription	Colonic Mucosa	Colon
31	chr3:47184000-47194200	Weak transcription	Spleen	Spleen
32	chr3:47184000-47197000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:47184400-47198400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:47184600-47192200	Weak transcription	Fetal Intestine Large	intestine
35	chr3:47184600-47194200	Weak transcription	Fetal Thymus	thymus
36	chr3:47184600-47194200	Weak transcription	Psoas Muscle	Psoas
37	chr3:47184600-47198000	Weak transcription	Thymus	Thymus
38	chr3:47184600-47202200	Weak transcription	Esophagus	oesophagus
39	chr3:47184800-47194000	Weak transcription	Ovary	ovary
40	chr3:47184800-47194200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:47184800-47197000	Weak transcription	Gastric	stomach
42	chr3:47184800-47199600	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr3:47184800-47199800	Weak transcription	Fetal Intestine Small	intestine
44	chr3:47185000-47193400	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:47186000-47194000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:47186800-47197000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:47187200-47192000	Weak transcription	Left Ventricle	heart
48	chr3:47187400-47193000	Weak transcription	Lung	lung
49	chr3:47187400-47193600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:47187400-47197200	Weak transcription	Right Atrium	heart

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