Variant report

Variant	rs8024027
Chromosome Location	chr15:93286926-93286927
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:93286354..93290416-chr15:93443311..93447414,3	MCF-7	breast:
2	chr15:93160927..93163023-chr15:93285555..93287552,2	MCF-7	breast:
3	chr15:93286706..93290050-chr15:93292782..93296311,3	MCF-7	breast:
4	chr15:93179390..93182218-chr15:93285466..93288131,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173575	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10459705	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10459706	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10459707	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11074097	0.92[CEU][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs11074099	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11074101	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11637781	0.95[EUR][1000 genomes]
rs12440115	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12593012	0.90[EUR][1000 genomes]
rs2388014	0.92[ASN][1000 genomes]
rs2388017	0.91[ASN][1000 genomes]
rs28708417	0.93[ASN][1000 genomes]
rs2892383	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6496987	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6496988	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7162785	0.96[ASN][1000 genomes]
rs7170266	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7170645	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7177207	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7178356	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7179340	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs8031853	0.83[EUR][1000 genomes]
rs8038242	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8038406	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs8040223	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8041271	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8041895	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8042841	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8043355	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9672507	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9672578	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
2	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
3	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
4	nsv1042292	chr15:93286333-93374887	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8024027	FAM174B	cis	cerebellum	SCAN
rs8024027	LOC400451	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93283000-93294400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr15:93285600-93287000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr15:93285600-93287200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:93285600-93287400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr15:93285600-93287400	Enhancers	H1 Cell Line	embryonic stem cell
6	chr15:93285600-93287400	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr15:93285800-93287000	Enhancers	Brain Germinal Matrix	brain
8	chr15:93286000-93287000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr15:93286000-93287000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr15:93286000-93287200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr15:93286000-93287200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:93286200-93287000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr15:93286800-93287000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
14	chr15:93286800-93287200	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr15:93286800-93287400	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr15:93286800-93289400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links