Variant report

Variant	rs4887161
Chromosome Location	chr15:74066556-74066557
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:74064186..74066703-chr15:74067930..74069882,2	MCF-7	breast:
2	chr15:74065767..74070891-chr15:74072493..74077043,5	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12440563	0.93[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12442096	0.91[AFR][1000 genomes]
rs17187183	0.84[AFR][1000 genomes]
rs2123208	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs28485305	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs28505607	0.81[AFR][1000 genomes]
rs28594180	0.89[AFR][1000 genomes]
rs28655328	0.81[AFR][1000 genomes]
rs28688071	0.94[ASN][1000 genomes]
rs28709470	0.82[AFR][1000 genomes]
rs3088341	0.82[AMR][1000 genomes]
rs3743098	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4243087	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4887111	0.82[AFR][1000 genomes]
rs4887164	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60833441	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7162423	0.86[ASW][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.82[AFR][1000 genomes]
rs7171779	0.86[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.92[ASN][1000 genomes]
rs7172656	0.86[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471252	chr15:74006691-74089793	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4887161	THAP10	cis	cerebellum	SCAN
rs4887161	COMMD4	cis	cerebellum	SCAN
rs4887161	ARIH1	cis	parietal	SCAN
rs4887161	SCAMP2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74053000-74067000	Weak transcription	Fetal Brain Male	brain
2	chr15:74060400-74067200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr15:74060800-74073000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr15:74061000-74076600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:74064200-74073200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr15:74064400-74067000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:74065200-74067000	Weak transcription	Esophagus	oesophagus
8	chr15:74065600-74067800	Enhancers	Left Ventricle	heart
9	chr15:74065800-74067600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:74066000-74066600	Enhancers	Brain Anterior Caudate	brain
11	chr15:74066000-74066800	Enhancers	Right Atrium	heart
12	chr15:74066000-74066800	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr15:74066000-74067600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:74066000-74076400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr15:74066200-74066600	Enhancers	Aorta	Aorta
16	chr15:74066200-74067000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr15:74066200-74067800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:74066200-74067800	Enhancers	Brain Germinal Matrix	brain
19	chr15:74066400-74066800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:74066400-74068000	Enhancers	Right Ventricle	heart
21	chr15:74066400-74073400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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