Variant report

Variant	rs6797460
Chromosome Location	chr3:67703509-67703510
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:67703041-67705477	IMR90	lung:	n/a	n/a
2	MEF2A	chr3:67703346-67704299	GM12878	blood:	n/a	chr3:67703875-67703889 chr3:67703870-67703891 chr3:67703877-67703888 chr3:67703874-67703889 chr3:67703858-67703866 chr3:67703874-67703890
3	POLR2A	chr3:67703060-67706271	HepG2	liver:	n/a	n/a
4	NFIC	chr3:67703316-67704366	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:67703465-67703572	MCF-7	breast:	n/a	n/a
6	POLR2A	chr3:67703304-67705555	GM12892	blood:	n/a	n/a
7	MTA3	chr3:67703325-67704527	GM12878	blood:	n/a	n/a
8	MXI1	chr3:67703457-67705425	GM12878	blood:	n/a	n/a
9	NFIC	chr3:67703409-67704816	GM12878	blood:	n/a	n/a
10	TBL1XR1	chr3:67703473-67705246	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:67703041-67705669	GM12891	blood:	n/a	n/a
12	BHLHE40	chr3:67703349-67705323	GM12878	blood:	n/a	chr3:67704778-67704794 chr3:67704889-67704905 chr3:67704881-67704897 chr3:67704875-67704891 chr3:67704716-67704732 chr3:67704724-67704740 chr3:67704897-67704913
13	RUNX3	chr3:67703363-67704653	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:67644182..67646267-chr3:67702951..67705002,2	MCF-7	breast:
2	chr3:67701996..67704573-chr3:67817178..67820032,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241316	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11707967	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11712921	0.85[EUR][1000 genomes]
rs11717561	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11719952	0.87[EUR][1000 genomes]
rs12714500	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13065696	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13068759	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13068996	0.84[EUR][1000 genomes]
rs13069212	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13069251	1.00[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13070332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13076100	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13077262	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081838	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13083820	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13086260	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13090197	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13091275	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13091330	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13092662	0.96[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13099253	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1376028	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1376029	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1376030	1.00[CEU][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1450345	0.92[EUR][1000 genomes]
rs1473351	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1814519	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1823476	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2167181	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2198015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2198016	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2218796	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2362453	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2362455	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62256429	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6766403	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6774971	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6778266	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6779395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786211	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787200	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6787642	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6787853	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6788874	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790771	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6791337	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6793868	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6797010	0.86[EUR][1000 genomes]
rs6798228	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6806285	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6806536	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6808106	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71621318	0.84[EUR][1000 genomes]
rs7434004	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7610446	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7615766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7632886	0.82[EUR][1000 genomes]
rs7639427	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7647518	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7653350	0.82[EUR][1000 genomes]
rs881948	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs881949	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs935734	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9811187	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470638	chr3:67367341-67814738	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv460700	chr3:67393629-67712970	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv590560	chr3:67393629-67712970	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv3359258	chr3:67589615-67828274	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv876922	chr3:67635506-67755257	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv428739	chr3:67656829-67730379	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6797460	RP11-81N13.1	cis	Thyroid	GTEx
rs6797460	RP11-81N13.1	cis	lung	GTEx
rs6797460	SUCLG2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67661200-67704000	Weak transcription	Fetal Kidney	kidney
2	chr3:67661400-67704000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:67661600-67703600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:67674000-67704000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:67681400-67703600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:67681800-67704200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:67686600-67703600	Weak transcription	Fetal Heart	heart
8	chr3:67686600-67704000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:67689600-67704000	Weak transcription	Thymus	Thymus
10	chr3:67695800-67703600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:67695800-67704000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:67697200-67703600	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr3:67697400-67704200	Enhancers	Small Intestine	intestine
14	chr3:67697600-67704200	Weak transcription	Lung	lung
15	chr3:67698000-67703600	Weak transcription	Fetal Stomach	stomach
16	chr3:67698200-67703800	Enhancers	Fetal Intestine Small	intestine
17	chr3:67698200-67704000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:67698400-67704000	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:67698400-67704200	Weak transcription	Placenta	Placenta
20	chr3:67698600-67703600	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr3:67698800-67704000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:67698800-67704200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:67699000-67704000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr3:67699000-67704000	Weak transcription	HMEC	breast
25	chr3:67699000-67704400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:67699200-67704000	Weak transcription	NH-A	brain
27	chr3:67699800-67703600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:67699800-67703600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr3:67699800-67703800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:67699800-67704000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:67699800-67704000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:67699800-67704000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr3:67699800-67704000	Weak transcription	HSMMtube	muscle
34	chr3:67700200-67704200	Enhancers	Primary B cells from peripheral blood	blood
35	chr3:67700400-67703600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr3:67700600-67704000	Enhancers	HepG2	liver
37	chr3:67700800-67703600	Flanking Active TSS	GM12878-XiMat	blood
38	chr3:67700800-67703800	Weak transcription	Brain Hippocampus Middle	brain
39	chr3:67700800-67704000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:67700800-67704000	Weak transcription	Psoas Muscle	Psoas
41	chr3:67701400-67704000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:67701400-67704200	Weak transcription	Ovary	ovary
43	chr3:67701600-67704200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:67701800-67703600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:67701800-67703600	Weak transcription	Colonic Mucosa	Colon
46	chr3:67701800-67703600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:67701800-67703600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:67701800-67704000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:67701800-67704000	Weak transcription	Right Ventricle	heart
50	chr3:67702000-67703600	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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