Variant report

Variant	rs1418201
Chromosome Location	chr6:142648056-142648057
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:142644240..142648928-chr6:142651290..142656139,5	MCF-7	breast:
2	chr6:142648035..142651499-chr6:142703981..142705983,3	MCF-7	breast:
3	chr6:142626055..142628342-chr6:142647346..142649184,2	MCF-7	breast:
4	chr6:142642940..142645383-chr6:142647071..142650024,3	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1040525	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1040526	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1342060	0.89[CEU][hapmap];0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1360194	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs155259	0.81[EUR][1000 genomes]
rs1891308	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2039986	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2039987	0.94[CEU][hapmap];0.86[CHB][hapmap];0.94[EUR][1000 genomes]
rs2050157	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294764	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2294771	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs262119	0.81[EUR][1000 genomes]
rs262121	0.81[EUR][1000 genomes]
rs262129	0.81[EUR][1000 genomes]
rs263180	0.81[EUR][1000 genomes]
rs263181	0.81[EUR][1000 genomes]
rs263182	0.81[EUR][1000 genomes]
rs263183	0.81[EUR][1000 genomes]
rs263184	0.81[EUR][1000 genomes]
rs263186	0.81[EUR][1000 genomes]
rs263187	0.81[EUR][1000 genomes]
rs263188	0.81[EUR][1000 genomes]
rs263189	0.81[EUR][1000 genomes]
rs3748069	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3817929	0.90[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4896582	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs6570507	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6570508	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs6570509	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6570510	0.89[CEU][hapmap];0.91[CHB][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6909857	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6929442	0.94[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6937121	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7741741	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7753012	0.90[CEU][hapmap]
rs7754638	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7755109	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7756305	0.89[CEU][hapmap];0.85[CHB][hapmap];0.93[EUR][1000 genomes]
rs7763064	0.86[EUR][1000 genomes]
rs7770386	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7774095	0.84[CEU][hapmap];0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7776375	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9373346	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9389984	0.94[EUR][1000 genomes]
rs9389985	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9389986	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9389987	0.92[EUR][1000 genomes]
rs9399401	0.90[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes]
rs9403380	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9403381	0.89[CEU][hapmap];0.85[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9403382	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9403383	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9403387	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9496346	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9496369	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9496374	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9496392	0.87[EUR][1000 genomes]
rs962554	0.95[CEU][hapmap];0.87[CHB][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs972982	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142624800-142651800	Weak transcription	HSMM	muscle
2	chr6:142626000-142650600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:142633200-142651000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:142635000-142651000	Weak transcription	NHEK	skin
5	chr6:142640400-142649800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:142640400-142652000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:142640600-142651200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:142643000-142653800	Weak transcription	Fetal Heart	heart
9	chr6:142645400-142650200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:142645400-142650600	Weak transcription	HMEC	breast
11	chr6:142646000-142652200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:142646000-142652600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr6:142646400-142652400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:142646400-142652400	Enhancers	HUVEC	blood vessel
15	chr6:142646600-142650000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:142647600-142648600	Enhancers	Fetal Lung	lung
17	chr6:142647600-142648600	Enhancers	NHLF	lung
18	chr6:142647800-142648200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:142647800-142648200	Enhancers	HepG2	liver
20	chr6:142647800-142649000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:142647800-142649000	Enhancers	Liver	Liver
22	chr6:142648000-142650400	Enhancers	A549	lung

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