Variant report

Variant	rs149947
Chromosome Location	chr6:27972433-27972434
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27972416..27975036-chr6:27975260..27977885,2	MCF-7	breast:
2	chr6:27965316..27968016-chr6:27970592..27972506,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs149899	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs149946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs149948	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs149961	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs149964	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs149968	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs149969	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs149970	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs149972	0.81[AFR][1000 genomes]
rs156736	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs156744	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs172166	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs175954	0.85[EUR][1000 genomes]
rs203890	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34171748	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs464312	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs469227	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66529373	0.81[EUR][1000 genomes]
rs9348789	0.82[EUR][1000 genomes]
rs9357060	0.82[EUR][1000 genomes]
rs9380045	0.82[EUR][1000 genomes]
rs9393881	0.82[EUR][1000 genomes]
rs9468271	0.82[EUR][1000 genomes]
rs9468274	0.82[EUR][1000 genomes]
rs9468275	0.82[EUR][1000 genomes]
rs9468277	0.82[EUR][1000 genomes]
rs9468278	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
2	nsv1022651	chr6:27864217-28017997	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv830619	chr6:27872302-28062544	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs149947	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs149947	AL022393.7	cis	Artery Aorta	GTEx
rs149947	RP1-265C24.5	cis	Muscle Skeletal	GTEx
rs149947	RP1-265C24.5	cis	Heart Left Ventricle	GTEx
rs149947	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs149947	OR2B8P	cis	Thyroid	GTEx
rs149947	AL022393.7	cis	Nerve Tibial	GTEx
rs149947	AL022393.7	cis	Muscle Skeletal	GTEx
rs149947	OR2B7P	cis	Thyroid	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27970800-27973800	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr6:27971000-27972600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:27971200-27973600	Enhancers	H1 Cell Line	embryonic stem cell
4	chr6:27971200-27974200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr6:27971400-27973400	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr6:27971600-27973200	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr6:27971800-27972600	Enhancers	Fetal Stomach	stomach
8	chr6:27971800-27973400	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr6:27971800-27973800	Enhancers	K562	blood
10	chr6:27971800-27974000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr6:27971800-27974000	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr6:27971800-27974800	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr6:27972000-27972800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:27972200-27972800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:27972200-27973400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:27972200-27973800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:27972400-27972600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr6:27972400-27973000	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links