Variant report

Variant	rs6766403
Chromosome Location	chr3:67698191-67698192
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:67692723..67696784-chr3:67696803..67701487,5	K562	blood:
2	chr3:67693746..67699726-chr3:67701571..67705130,8	K562	blood:
3	chr3:67693669..67696019-chr3:67696200..67698241,3	MCF-7	breast:
4	chr3:67697874..67699560-chr3:67705440..67708186,2	K562	blood:
5	chr3:67696995..67702204-chr3:67702925..67706326,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172340	Chromatin interaction
ENSG00000241316	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11707967	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11712921	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11717561	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11719952	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12714500	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13065696	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13068759	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13068996	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13069212	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13069251	1.00[CEU][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13070332	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13076100	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13077262	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13081838	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13083820	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13086260	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13090197	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13091275	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13091330	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13092662	0.96[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13099253	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1376028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1376029	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1376030	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1450345	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1473351	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1814519	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1823476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2167181	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2198015	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2198016	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2218796	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2362453	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2362454	0.81[AMR][1000 genomes]
rs2362455	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62256429	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6774971	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6778266	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6779395	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]
rs6786211	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6787200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6787642	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6787853	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6788874	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6790771	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6791337	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6793868	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6797010	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6797460	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]
rs6798228	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6806285	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6806536	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6808106	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71621318	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7434004	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610446	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7615766	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7632886	0.82[EUR][1000 genomes]
rs7639427	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7647518	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7653350	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs881948	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs881949	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs935734	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9811187	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6766403	RP11-81N13.1	cis	Thyroid	GTEx
rs6766403	SUCLG2	cis	multi-tissue	Pritchard
rs6766403	LRIG1	cis	parietal	SCAN
rs6766403	SUCLG2	cis	lymphoblastoid	seeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67631400-67700200	Weak transcription	K562	blood
2	chr3:67661200-67704000	Weak transcription	Fetal Kidney	kidney
3	chr3:67661400-67699400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:67661400-67700000	Weak transcription	Ovary	ovary
5	chr3:67661400-67701000	Weak transcription	Fetal Lung	lung
6	chr3:67661400-67704000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:67661600-67703600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:67668400-67699600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:67670200-67703400	Weak transcription	Aorta	Aorta
10	chr3:67670600-67699000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:67670800-67703200	Weak transcription	Adipose Nuclei	Adipose
12	chr3:67671000-67700600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:67673800-67703400	Weak transcription	Fetal Thymus	thymus
14	chr3:67674000-67704000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr3:67681400-67703600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:67681800-67698800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:67681800-67704200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:67686200-67698200	Weak transcription	Right Ventricle	heart
19	chr3:67686600-67703600	Weak transcription	Fetal Heart	heart
20	chr3:67686600-67704000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:67686800-67698600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:67686800-67703400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr3:67686800-67703400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:67687800-67703400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:67688000-67703400	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr3:67689400-67700600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:67689600-67704000	Weak transcription	Thymus	Thymus
28	chr3:67690800-67700200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:67691800-67700800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:67692200-67699200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:67692200-67699600	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:67692800-67699800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:67693400-67700000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr3:67693400-67703400	Weak transcription	Brain Substantia Nigra	brain
35	chr3:67693600-67698400	Strong transcription	Primary B cells from cord blood	blood
36	chr3:67694200-67700200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr3:67695800-67703600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:67695800-67704000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr3:67696200-67698200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr3:67696400-67698200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr3:67696600-67698400	Strong transcription	Fetal Muscle Leg	muscle
42	chr3:67696600-67698400	Enhancers	Spleen	Spleen
43	chr3:67696600-67701800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:67696800-67702400	Enhancers	Fetal Intestine Large	intestine
45	chr3:67697000-67698400	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr3:67697000-67698600	Strong transcription	Primary T cells from cord blood	blood
47	chr3:67697000-67700000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:67697000-67700800	Enhancers	Osteobl	bone
49	chr3:67697000-67701400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:67697200-67698200	Enhancers	Primary T helper naive cells from peripheral blood	blood

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