Variant report

Variant	rs230721
Chromosome Location	chr14:65318130-65318131
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:65318120..65320301-chr14:65322198..65325013,2	MCF-7	breast:
2	chr14:65317600..65319919-chr14:65379346..65381872,2	MCF-7	breast:
3	chr14:65306058..65308869-chr14:65317790..65319964,2	MCF-7	breast:
4	chr14:65310132..65314457-chr14:65315119..65319141,7	K562	blood:
5	chr14:65309823..65312590-chr14:65316420..65318334,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258289	Chromatin interaction
ENSG00000125954	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1003370	0.97[EUR][1000 genomes]
rs10151551	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10162522	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1122339	0.97[EUR][1000 genomes]
rs11844283	0.82[EUR][1000 genomes]
rs12147448	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1951489	0.82[EUR][1000 genomes]
rs1957422	0.82[EUR][1000 genomes]
rs1957430	0.97[EUR][1000 genomes]
rs1957433	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.97[EUR][1000 genomes]
rs1983769	0.82[EUR][1000 genomes]
rs2104170	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs230722	1.00[CEU][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs368818	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs374461	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs375797	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs378391	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs3813424	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs389370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs395112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs397901	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs399508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs406811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs424222	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs426044	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs435006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs435335	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4899150	0.82[MEX][hapmap]
rs4899151	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4902323	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4902324	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58989463	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61989891	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6573584	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[AMR][1000 genomes]
rs7149121	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7149446	0.82[EUR][1000 genomes]
rs7158624	0.82[EUR][1000 genomes]
rs762072	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8008229	0.97[EUR][1000 genomes]
rs8013371	0.92[EUR][1000 genomes]
rs8022462	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9323455	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9323456	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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	esv3693408	chr14:65292670-65358576	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs230721	MARCO	trans	brain	seeQTL
rs230721	SCGB2A2	trans	brain	seeQTL
rs230721	CHURC1	cis	lymphoblastoid	seeQTL
rs230721	FNTB	cis	lymphoblastoid	seeQTL
rs230721	SCGB1D2	trans	brain	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65311800-65318200	Enhancers	Skeletal Muscle Female	skeletal muscle
2	chr14:65314600-65318800	Weak transcription	Right Atrium	heart
3	chr14:65314800-65318800	Weak transcription	Fetal Heart	heart
4	chr14:65314800-65319000	Weak transcription	Right Ventricle	heart
5	chr14:65315000-65318800	Weak transcription	K562	blood
6	chr14:65315400-65324600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr14:65316600-65318200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr14:65317400-65318800	Weak transcription	Left Ventricle	heart
9	chr14:65317400-65320000	Weak transcription	Psoas Muscle	Psoas
10	chr14:65318000-65318400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
11	chr14:65318000-65318400	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
12	chr14:65318000-65319400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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