Variant report

Variant	rs6779395
Chromosome Location	chr3:67701430-67701431
allele	A/T
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	chr3:67701165-67702808	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:67701243-67702529	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr3:67700890-67701604	HepG2	liver:	n/a	n/a
4	EBF1	chr3:67701243-67701471	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:67692723..67696784-chr3:67696803..67701487,5	K562	blood:
2	chr3:67696995..67702204-chr3:67702925..67706326,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241316	TF binding region
ENSG00000241316	Chromatin interaction
ENSG00000172340	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11707967	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11712921	0.85[EUR][1000 genomes]
rs11717561	0.85[EUR][1000 genomes]
rs11719952	0.87[EUR][1000 genomes]
rs12714500	0.85[AFR][1000 genomes];0.95[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];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13068759	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13068996	0.84[EUR][1000 genomes]
rs13069212	0.91[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];0.92[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];0.97[YRI][hapmap];0.82[AFR][1000 genomes];0.88[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];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13077262	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081838	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13083820	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13086260	0.85[EUR][1000 genomes]
rs13090197	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13091275	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13091330	0.89[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];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13099253	0.89[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];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.97[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];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1376030	1.00[CEU][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1450345	0.92[EUR][1000 genomes]
rs1473351	0.82[EUR][1000 genomes]
rs1814519	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1823476	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2167181	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2198015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2198016	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2218796	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2362453	0.97[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];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62256429	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6766403	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6774971	0.86[EUR][1000 genomes]
rs6778266	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6786211	0.84[AFR][1000 genomes];0.97[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];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6787642	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6787853	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6788874	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790771	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6791337	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6793868	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6797010	0.86[EUR][1000 genomes]
rs6797460	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]
rs6798228	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.88[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];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6806536	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6808106	0.86[EUR][1000 genomes]
rs71621318	0.84[EUR][1000 genomes]
rs7434004	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7610446	0.88[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];0.86[AFR][1000 genomes];0.95[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];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7647518	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7653350	0.82[EUR][1000 genomes]
rs881948	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs881949	0.83[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];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9811187	0.83[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6779395	SUCLG2	Cis_1M	lymphoblastoid	RTeQTL
rs6779395	RP11-81N13.1	cis	Thyroid	GTEx

Chromatin state (count:108 , 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	chr3:67670200-67703400	Weak transcription	Aorta	Aorta
5	chr3:67670800-67703200	Weak transcription	Adipose Nuclei	Adipose
6	chr3:67673800-67703400	Weak transcription	Fetal Thymus	thymus
7	chr3:67674000-67704000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:67681400-67703600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:67681800-67704200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:67686600-67703600	Weak transcription	Fetal Heart	heart
11	chr3:67686600-67704000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:67686800-67703400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:67686800-67703400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:67687800-67703400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:67688000-67703400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr3:67689600-67704000	Weak transcription	Thymus	Thymus
17	chr3:67693400-67703400	Weak transcription	Brain Substantia Nigra	brain
18	chr3:67695800-67703600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:67695800-67704000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:67696600-67701800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:67696800-67702400	Enhancers	Fetal Intestine Large	intestine
22	chr3:67697200-67702000	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr3:67697200-67703600	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr3:67697400-67704200	Enhancers	Small Intestine	intestine
25	chr3:67697600-67701600	Weak transcription	Esophagus	oesophagus
26	chr3:67697600-67702000	Enhancers	Right Atrium	heart
27	chr3:67697600-67704200	Weak transcription	Lung	lung
28	chr3:67698000-67703000	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr3:67698000-67703600	Weak transcription	Fetal Stomach	stomach
30	chr3:67698200-67701800	Enhancers	Right Ventricle	heart
31	chr3:67698200-67703200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr3:67698200-67703800	Enhancers	Fetal Intestine Small	intestine
33	chr3:67698200-67704000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:67698400-67704000	Weak transcription	Fetal Muscle Leg	muscle
35	chr3:67698400-67704200	Weak transcription	Placenta	Placenta
36	chr3:67698600-67701800	Genic enhancers	Primary T cells from cord blood	blood
37	chr3:67698600-67702400	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr3:67698600-67703400	Weak transcription	HUVEC	blood vessel
39	chr3:67698600-67703600	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr3:67698800-67701600	Enhancers	Muscle Satellite Cultured Cells	--
41	chr3:67698800-67702200	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr3:67698800-67703200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:67698800-67703400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr3:67698800-67704000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:67698800-67704200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:67699000-67703200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:67699000-67704000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr3:67699000-67704000	Weak transcription	HMEC	breast
49	chr3:67699000-67704400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:67699200-67704000	Weak transcription	NH-A	brain

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