Variant report

Variant	rs12402128
Chromosome Location	chr1:85864711-85864712
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85773623..85774572-chr1:85864125..85865314,5	MCF-7	breast:
2	chr1:85863358..85866240-chr1:85910699..85913658,2	K562	blood:
3	chr1:85809642..85811064-chr1:85864019..85865015,8	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CYR61-3	chr1:85864140-85865646	ENSG00000223653

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10493764	0.95[CEU][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13373844	0.81[CEU][hapmap]
rs1523993	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17387935	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17590006	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs35092233	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35294786	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35876501	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35956189	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36062892	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3768226	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4475804	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61769490	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61783046	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6659486	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6673833	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7540393	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7555486	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription 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	12 gene(s)	inside rSNPs	diseases
3	nsv1008877	chr1:85843238-85897570	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3393958	chr1:85857980-85874598	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85845000-85870000	Weak transcription	HSMMtube	muscle
2	chr1:85855200-85870000	Weak transcription	Fetal Stomach	stomach
3	chr1:85856000-85872800	Weak transcription	Fetal Intestine Small	intestine
4	chr1:85859400-85865000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:85861600-85865800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:85861800-85865800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:85862000-85864800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr1:85862200-85874600	Weak transcription	Pancreas	Pancrea
9	chr1:85862600-85865000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:85862600-85869000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:85862800-85865200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr1:85862800-85865400	Enhancers	Fetal Lung	lung
13	chr1:85862800-85866200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr1:85862800-85866200	Enhancers	NHLF	lung
15	chr1:85862800-85867000	Enhancers	Liver	Liver
16	chr1:85863000-85865800	Enhancers	Muscle Satellite Cultured Cells	--
17	chr1:85863200-85865400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:85863400-85864800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:85863400-85865000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:85863400-85865400	Enhancers	HUVEC	blood vessel
21	chr1:85863400-85865400	Enhancers	NHDF-Ad	bronchial
22	chr1:85863400-85866400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:85863600-85865600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:85863600-85867000	Genic enhancers	Osteobl	bone
25	chr1:85864000-85872600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:85864200-85865400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:85864200-85865400	Genic enhancers	HSMM	muscle
28	chr1:85864400-85865000	Weak transcription	Psoas Muscle	Psoas
29	chr1:85864400-85865400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:85864400-85866400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:85864400-85869800	Weak transcription	Aorta	Aorta
32	chr1:85864400-85870600	Weak transcription	Fetal Muscle Leg	muscle
33	chr1:85864400-85871000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr1:85864400-85871800	Weak transcription	NH-A	brain
35	chr1:85864400-85872200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:85864400-85873000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:85864400-85874600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:85864600-85864800	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr1:85864600-85864800	Weak transcription	Ovary	ovary
40	chr1:85864600-85865000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:85864600-85870000	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links