Variant report

Variant	rs6791213
Chromosome Location	chr3:161033721-161033722
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:161030291..161037720-chr3:161038093..161046558,15	MCF-7	breast:
2	chr3:161033236..161036164-chr3:161124055..161126623,3	MCF-7	breast:
3	chr3:61852002..61854331-chr3:161033145..161035721,2	MCF-7	breast:
4	chr3:161031627..161035949-chr3:161055362..161059558,6	MCF-7	breast:
5	chr3:160987464..160989480-chr3:161032587..161035559,2	MCF-7	breast:
6	chr3:160998590..161004098-chr3:161031167..161035957,5	MCF-7	breast:
7	chr3:161031670..161034485-chr3:161051893..161053628,2	MCF-7	breast:
8	chr3:161030909..161038608-chr3:161038848..161046580,20	MCF-7	breast:
9	chr3:161021008..161023752-chr3:161033340..161034847,2	MCF-7	breast:
10	chr3:161032948..161035717-chr3:161058882..161060875,3	MCF-7	breast:
11	chr3:161007104..161011008-chr3:161031241..161034660,5	MCF-7	breast:
12	chr3:161006401..161012112-chr3:161031973..161037314,13	MCF-7	breast:
13	chr3:161025819..161030681-chr3:161030815..161036788,8	MCF-7	breast:
14	chr3:160991428..160993713-chr3:161032397..161034859,2	MCF-7	breast:
15	chr3:161026928..161036306-chr3:161081784..161094254,31	MCF-7	breast:
16	chr3:160995569..160997087-chr3:161032964..161034982,2	MCF-7	breast:
17	chr3:161031194..161033997-chr3:161131950..161133763,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction
ENSG00000240138	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10804790	0.81[EUR][1000 genomes]
rs10936223	0.83[AMR][1000 genomes]
rs10936224	0.86[AMR][1000 genomes]
rs1154701	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs12486253	0.95[EUR][1000 genomes]
rs12495310	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12631850	0.83[AMR][1000 genomes]
rs13083229	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1382427	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs1382428	0.80[EUR][1000 genomes]
rs1478565	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs1478568	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs1600209	0.81[EUR][1000 genomes]
rs163328	0.82[CEU][hapmap]
rs189270	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs1993891	0.82[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs336541	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs336543	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs336548	0.81[EUR][1000 genomes]
rs336567	0.82[CEU][hapmap]
rs336568	0.82[EUR][1000 genomes]
rs336570	0.82[CEU][hapmap]
rs336572	0.85[CEU][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs336577	0.82[CEU][hapmap]
rs336580	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs336582	0.82[EUR][1000 genomes]
rs336583	0.82[CEU][hapmap]
rs336585	0.82[CEU][hapmap]
rs336586	0.85[CEU][hapmap]
rs336589	0.88[CEU][hapmap]
rs336590	0.89[CEU][hapmap]
rs336591	0.88[CEU][hapmap]
rs336593	0.85[CEU][hapmap]
rs339101	0.81[CEU][hapmap]
rs3849524	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs4273380	0.82[CEU][hapmap]
rs4290817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4370045	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs4470535	0.94[EUR][1000 genomes]
rs4493449	0.82[CEU][hapmap]
rs4518145	0.83[EUR][1000 genomes]
rs4560315	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs456611	0.82[CEU][hapmap]
rs4597724	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs460508	0.82[CEU][hapmap]
rs462514	0.96[CEU][hapmap]
rs463928	0.81[CEU][hapmap]
rs464766	0.82[CEU][hapmap]
rs4856714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4856738	0.94[EUR][1000 genomes]
rs4856739	0.85[EUR][1000 genomes]
rs4856767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4856768	0.95[EUR][1000 genomes]
rs55688744	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6441370	0.86[EUR][1000 genomes]
rs6441371	0.84[EUR][1000 genomes]
rs6441373	0.82[CEU][hapmap]
rs6765269	0.81[CEU][hapmap]
rs6768818	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6774276	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs6775627	0.81[CEU][hapmap]
rs6789388	0.96[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs6794601	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs6809256	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7611367	0.96[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs7613227	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7613358	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7615592	0.82[CEU][hapmap]
rs7623206	0.82[CEU][hapmap]
rs7627528	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7632797	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs7633186	0.96[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs7636941	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7638668	0.81[EUR][1000 genomes]
rs7652267	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7653361	0.82[CEU][hapmap]
rs899275	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809522	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9815222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9821201	0.82[CEU][hapmap]
rs9834659	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9839527	0.95[EUR][1000 genomes]
rs9850455	0.82[CEU][hapmap]
rs9864752	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9872514	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs9879687	0.83[AMR][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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv829770	chr3:160989573-161069223	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv4091	chr3:161018540-161063875	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6791213	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL
rs6791213	PPM1L	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161031800-161034400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr3:161032400-161034800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:161032600-161034000	Enhancers	GM12878-XiMat	blood
4	chr3:161032600-161034200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:161032600-161034800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr3:161032600-161035000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:161032600-161035000	Enhancers	Hela-S3	cervix
8	chr3:161032600-161035000	Enhancers	NHEK	skin
9	chr3:161032600-161035200	Enhancers	HUVEC	blood vessel
10	chr3:161032800-161034000	Enhancers	Small Intestine	intestine
11	chr3:161032800-161034600	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr3:161032800-161034800	Enhancers	HMEC	breast
13	chr3:161032800-161035000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr3:161033000-161034200	Weak transcription	NH-A	brain
15	chr3:161033000-161035000	Enhancers	Stomach Mucosa	stomach
16	chr3:161033200-161034400	Weak transcription	NHDF-Ad	bronchial
17	chr3:161033400-161034800	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr3:161033600-161034200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:161033600-161034400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:161033600-161035000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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