Variant report

Variant	rs12254238
Chromosome Location	chr10:98099765-98099766
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:97776713..97777777-chr10:98099654..98100263,3	K562	blood:
2	chr10:97988986..97990030-chr10:98099646..98100689,10	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10218881	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10748671	0.81[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs10786280	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882772	0.88[CEU][hapmap]
rs10882775	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882779	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10882781	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs11188709	0.82[CEU][hapmap]
rs11188722	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188724	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188725	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188726	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188731	0.81[JPT][hapmap]
rs11591467	0.88[CEU][hapmap]
rs11593073	0.82[CEU][hapmap]
rs11593074	0.89[CEU][hapmap]
rs11597348	0.89[CEU][hapmap]
rs12242936	0.81[JPT][hapmap]
rs12570008	0.81[JPT][hapmap]
rs12571241	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12572329	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17111733	0.85[CEU][hapmap]
rs17111736	0.81[JPT][hapmap]
rs1923704	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1923706	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146392	0.80[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2146393	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273891	0.88[CEU][hapmap]
rs2861572	0.88[CEU][hapmap]
rs2861574	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901989	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814224	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818313	0.88[CEU][hapmap]
rs4424609	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4917732	0.88[CEU][hapmap]
rs7077344	0.88[CEU][hapmap]
rs7085949	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7096643	0.84[EUR][1000 genomes];1.00[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	esv3413353	chr10:98039370-98561524	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv831950	chr10:98080972-98245434	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98095200-98099800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr10:98095200-98101200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr10:98097200-98099800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr10:98097400-98099800	Enhancers	Brain Angular Gyrus	brain
5	chr10:98097400-98099800	Weak transcription	Fetal Thymus	thymus
6	chr10:98097800-98099800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr10:98098000-98101600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr10:98098400-98101600	Enhancers	Brain Hippocampus Middle	brain
9	chr10:98098400-98101600	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr10:98098600-98100200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr10:98098600-98101200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr10:98098800-98099800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr10:98098800-98100800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr10:98098800-98101200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr10:98099000-98100400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr10:98099000-98100800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr10:98099000-98100800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr10:98099000-98101200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr10:98099000-98101200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr10:98099200-98101600	Enhancers	Brain Substantia Nigra	brain
21	chr10:98099400-98099800	Weak transcription	Dnd41	blood
22	chr10:98099400-98100200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr10:98099400-98100800	Weak transcription	Thymus	Thymus
24	chr10:98099600-98101000	Weak transcription	Brain Anterior Caudate	brain
25	chr10:98099600-98102000	Enhancers	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links