Variant report

Variant	rs6798228
Chromosome Location	chr3:67693480-67693481
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:67689171..67691000-chr3:67691714..67693901,2	MCF-7	breast:
2	chr3:67692273..67695539-chr3:67703678..67707123,3	MCF-7	breast:
3	chr3:67692723..67696784-chr3:67696803..67701487,5	K562	blood:

Variant related genes	Relation type
ENSG00000172340	Chromatin interaction
ENSG00000241316	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11707967	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11712921	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11717561	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11719952	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12714500	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13065696	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13068759	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13068996	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13069212	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13069251	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13070332	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13076100	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13077262	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13081838	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13083820	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13086260	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13090197	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13091275	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13091330	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13092662	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13099253	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1376028	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1376029	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1376030	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1450345	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1473351	0.81[AMR][1000 genomes]
rs1814519	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1823476	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2167181	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2198015	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2198016	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2218796	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2362453	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2362455	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62256429	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6766403	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]
rs6774971	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6778266	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779395	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]
rs6786211	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6787200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787642	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6787853	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6788874	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6790771	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6791337	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6793868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794625	0.85[EUR][1000 genomes]
rs6797010	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6797460	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];0.87[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6806536	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6808106	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71621318	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7434004	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7610446	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7615766	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7639427	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7644842	0.81[ASN][1000 genomes]
rs7647518	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7653350	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs881948	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs881949	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs935734	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];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9811187	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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
rs6798228	SUCLG2	cis	multi-tissue	Pritchard
rs6798228	RP11-81N13.1	cis	Thyroid	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67612400-67697200	Weak transcription	Hela-S3	cervix
2	chr3:67631400-67700200	Weak transcription	K562	blood
3	chr3:67659800-67697400	Weak transcription	Colonic Mucosa	Colon
4	chr3:67660000-67697200	Weak transcription	Lung	lung
5	chr3:67660000-67697400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:67661200-67704000	Weak transcription	Fetal Kidney	kidney
7	chr3:67661400-67699400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:67661400-67700000	Weak transcription	Ovary	ovary
9	chr3:67661400-67701000	Weak transcription	Fetal Lung	lung
10	chr3:67661400-67704000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:67661600-67703600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:67668400-67699600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:67668600-67696600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:67670200-67703400	Weak transcription	Aorta	Aorta
15	chr3:67670400-67694000	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:67670600-67696200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:67670600-67699000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:67670800-67703200	Weak transcription	Adipose Nuclei	Adipose
19	chr3:67671000-67700600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:67671800-67697800	Weak transcription	Dnd41	blood
21	chr3:67673800-67696800	Weak transcription	Fetal Intestine Large	intestine
22	chr3:67673800-67703400	Weak transcription	Fetal Thymus	thymus
23	chr3:67674000-67696600	Weak transcription	Fetal Stomach	stomach
24	chr3:67674000-67704000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr3:67681400-67703600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr3:67681800-67695600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:67681800-67698800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:67681800-67704200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:67684800-67697200	Weak transcription	Esophagus	oesophagus
30	chr3:67685400-67697600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr3:67685800-67695400	Weak transcription	HUVEC	blood vessel
32	chr3:67685800-67697200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr3:67686200-67697200	Weak transcription	Stomach Mucosa	stomach
34	chr3:67686200-67698200	Weak transcription	Right Ventricle	heart
35	chr3:67686400-67696600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:67686400-67696600	Weak transcription	Right Atrium	heart
37	chr3:67686600-67697200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:67686600-67697200	Weak transcription	HMEC	breast
39	chr3:67686600-67697200	Weak transcription	NHLF	lung
40	chr3:67686600-67703600	Weak transcription	Fetal Heart	heart
41	chr3:67686600-67704000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr3:67686800-67697200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:67686800-67698600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:67686800-67703400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr3:67686800-67703400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr3:67687800-67703400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:67688000-67703400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr3:67688200-67697000	Weak transcription	GM12878-XiMat	blood
49	chr3:67688400-67697200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:67688600-67694600	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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