Variant report

Variant	rs6488357
Chromosome Location	chr12:11331973-11331974
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:11326790..11329345-chr12:11330898..11332485,3	K562	blood:
2	chr12:11331591..11333492-chr12:11338114..11339808,2	K562	blood:
3	chr12:11330504..11332010-chr12:11332108..11333745,2	K562	blood:
4	chr12:11321748..11327565-chr12:11327784..11333912,14	MCF-7	breast:
5	chr12:11326790..11329345-chr12:11330898..11332446,2	K562	blood:

Variant related genes	Relation type
ENSG00000111215	Chromatin interaction
ENSG00000256629	Chromatin interaction
ENSG00000186136	Chromatin interaction
ENSG00000256712	Chromatin interaction
ENSG00000212127	Chromatin interaction
ENSG00000256537	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 42 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1047709	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1047712	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1349553	0.84[ASN][1000 genomes]
rs1451765	0.82[ASN][1000 genomes]
rs1451766	1.00[ASN][1000 genomes]
rs1451772	0.82[ASN][1000 genomes]
rs1451774	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1551191	0.81[ASN][1000 genomes]
rs1551193	0.84[ASN][1000 genomes]
rs1650020	0.82[ASN][1000 genomes]
rs1650029	0.81[ASN][1000 genomes]
rs1650030	0.82[ASN][1000 genomes]
rs1650031	0.82[ASN][1000 genomes]
rs1650053	0.81[ASN][1000 genomes]
rs1669410	0.82[ASN][1000 genomes]
rs1669412	0.82[ASN][1000 genomes]
rs1669414	0.82[ASN][1000 genomes]
rs1669418	0.82[ASN][1000 genomes]
rs1669422	0.82[ASN][1000 genomes]
rs17817150	1.00[ASN][1000 genomes]
rs1817104	0.82[ASN][1000 genomes]
rs1863848	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2290318	0.84[ASN][1000 genomes]
rs2290319	0.84[ASN][1000 genomes]
rs2416548	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2416549	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708331	0.82[ASN][1000 genomes]
rs319267	0.82[ASN][1000 genomes]
rs319268	0.82[ASN][1000 genomes]
rs319271	0.82[ASN][1000 genomes]
rs319272	0.82[ASN][1000 genomes]
rs319273	0.82[ASN][1000 genomes]
rs319274	0.82[ASN][1000 genomes]
rs34134804	1.00[ASN][1000 genomes]
rs34272839	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34373518	0.83[ASN][1000 genomes]
rs34413287	0.92[ASN][1000 genomes]
rs34648613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34666803	0.84[ASN][1000 genomes]
rs34708147	0.81[ASN][1000 genomes]
rs34949195	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35119575	0.81[ASN][1000 genomes]
rs35183723	0.81[ASN][1000 genomes]
rs35499317	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35650731	1.00[ASN][1000 genomes]
rs35746980	0.84[ASN][1000 genomes]
rs35969491	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3863325	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3911234	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4101885	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4583064	0.96[ASN][1000 genomes]
rs4763638	0.81[ASN][1000 genomes]
rs5020531	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488346	0.83[ASN][1000 genomes]
rs6488358	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67471783	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67955183	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132674	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136602	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71453440	1.00[ASN][1000 genomes]
rs7302711	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316032	0.83[ASN][1000 genomes]
rs7350611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7488095	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7488102	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7976950	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980677	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758294	chr12:10969620-11714921	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	esv2759879	chr12:10969620-11714921	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
3	nsv1038277	chr12:11060978-11504091	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv428272	chr12:11069845-11714921	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv898783	chr12:11185236-11338781	ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv898784	chr12:11188140-11341521	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv1050050	chr12:11192046-11436359	Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	nsv1053783	chr12:11203509-11495584	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
9	esv1807067	chr12:11214215-11568895	Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:42)

SNP	Gene	Cis/trans	Tissue	Source
rs6488357	RP11-434C1.1	cis	Nerve Tibial	GTEx
rs6488357	TAS2R14	cis	Nerve Tibial	GTEx
rs6488357	TAS2R14	cis	Esophagus Muscularis	GTEx
rs6488357	RP11-434C1.1	cis	Adipose Subcutaneous	GTEx
rs6488357	TAS2R20	cis	Esophagus Muscularis	GTEx
rs6488357	RP11-785H5.1	cis	Muscle Skeletal	GTEx
rs6488357	RP11-434C1.1	cis	Skin Sun Exposed Lower leg	GTEx
rs6488357	RP11-434C1.1	cis	Esophagus Muscularis	GTEx
rs6488357	RP11-434C1.1	cis	Artery Tibial	GTEx
rs6488357	PRR4	cis	Nerve Tibial	GTEx
rs6488357	TAS2R20	cis	lung	GTEx
rs6488357	RP11-434C1.1	cis	Artery Aorta	GTEx
rs6488357	PRR4	cis	Muscle Skeletal	GTEx
rs6488357	TAS2R20	cis	Nerve Tibial	GTEx
rs6488357	PRR4	cis	Artery Tibial	GTEx
rs6488357	TAS2R14	cis	Esophagus Mucosa	GTEx
rs6488357	TAS2R20	cis	Artery Tibial	GTEx
rs6488357	TAS2R14	cis	Muscle Skeletal	GTEx
rs6488357	TAS2R20	cis	Thyroid	GTEx
rs6488357	TAS2R20	cis	Esophagus Mucosa	GTEx
rs6488357	RP11-434C1.1	cis	Esophagus Mucosa	GTEx
rs6488357	RP11-434C1.1	cis	lung	GTEx
rs6488357	TAS2R20	cis	Adipose Subcutaneous	GTEx
rs6488357	TAS2R15	cis	Thyroid	GTEx
rs6488357	PRR4	cis	lung	GTEx
rs6488357	PRR4	cis	Heart Left Ventricle	GTEx
rs6488357	PRR4	cis	Adipose Subcutaneous	GTEx
rs6488357	RP11-434C1.1	cis	Thyroid	GTEx
rs6488357	TAS2R14	cis	Skin Sun Exposed Lower leg	GTEx
rs6488357	RP11-434C1.1	cis	Heart Left Ventricle	GTEx
rs6488357	TAS2R20	cis	Skin Sun Exposed Lower leg	GTEx
rs6488357	TAS2R14	cis	Thyroid	GTEx
rs6488357	TAS2R14	cis	lung	GTEx
rs6488357	TAS2R14	cis	Artery Tibial	GTEx
rs6488357	PRR4	cis	multi-tissue	Pritchard
rs6488357	TAS2R20	cis	Muscle Skeletal	GTEx
rs6488357	PRR4	cis	Esophagus Muscularis	GTEx
rs6488357	PRR4	cis	Thyroid	GTEx
rs6488357	RP11-434C1.1	cis	Muscle Skeletal	GTEx
rs6488357	PRR4	cis	Whole Blood	GTEx
rs6488357	RP11-434C1.1	cis	Stomach	GTEx
rs6488357	TAS2R14	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11325000-11335600	Weak transcription	Left Ventricle	heart
2	chr12:11325200-11332200	Weak transcription	Fetal Muscle Leg	muscle
3	chr12:11325200-11332200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:11325400-11332000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr12:11325600-11332200	Weak transcription	Brain Germinal Matrix	brain
6	chr12:11325600-11334400	Weak transcription	Primary B cells from cord blood	blood
7	chr12:11325600-11338200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr12:11326000-11334400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr12:11326200-11334600	Weak transcription	Liver	Liver
10	chr12:11326200-11338600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr12:11326400-11332000	Weak transcription	NHEK	skin
12	chr12:11326400-11334400	Weak transcription	Fetal Thymus	thymus
13	chr12:11326400-11337400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:11326400-11355600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:11328000-11338600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:11328600-11332200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:11328600-11334400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:11328800-11340400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:11329200-11332000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr12:11330600-11365400	Weak transcription	Primary T cells from cord blood	blood
21	chr12:11331200-11332400	Enhancers	GM12878-XiMat	blood

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