Variant report

Variant	rs1399916
Chromosome Location	chr3:161359375-161359376
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:161354917..161360014-chr3:161360082..161365935,6	MCF-7	breast:
2	chr3:161355978..161357623-chr3:161357960..161359774,3	MCF-7	breast:
3	chr3:161358345..161359934-chr3:161364741..161367383,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1399906	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1399908	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1399909	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1399910	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1399913	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1399915	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1515725	0.80[ASN][1000 genomes]
rs1515741	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1515743	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1568020	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1588908	0.80[ASN][1000 genomes]
rs16832928	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1849999	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1850000	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1878064	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2203490	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2222055	0.80[ASN][1000 genomes]
rs4305435	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4472057	0.80[ASN][1000 genomes]
rs4856709	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4856712	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441393	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441395	0.80[ASN][1000 genomes]
rs6762110	0.84[CEU][hapmap]
rs6781716	0.86[EUR][1000 genomes]
rs6793693	0.86[EUR][1000 genomes]
rs6809783	0.80[ASN][1000 genomes]
rs7620901	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7621711	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7629214	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641444	0.88[EUR][1000 genomes]
rs7652034	0.80[ASN][1000 genomes]
rs9290088	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9820806	0.80[ASN][1000 genomes]
rs9829196	0.80[ASN][1000 genomes]
rs9859298	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9867300	0.80[ASN][1000 genomes]
rs9868834	0.86[EUR][1000 genomes]
rs9871565	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9872386	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9876363	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9876608	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9877938	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9879265	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9879283	0.80[ASN][1000 genomes]
rs9883089	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
2	nsv829774	chr3:161229405-161386919	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv2422309	chr3:161242389-161425932	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv877711	chr3:161275848-161486665	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1004255	chr3:161340249-161476537	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv2755105	chr3:161349991-161371789	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
7	esv2754526	chr3:161353644-161371789	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
8	nsv1012553	chr3:161354221-161371789	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161356000-161362800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr3:161356600-161360800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:161358400-161361800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:161358800-161361000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:161359000-161360600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:161359000-161361000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:161359200-161360400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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