Variant report

Variant	rs9864752
Chromosome Location	chr3:160937591-160937592
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr3:160937373-160937595	Hela-S3	cervix:	n/a	n/a
2	REST	chr3:160937300-160937593	Hela-S3	cervix:	n/a	n/a
3	REST	chr3:160937304-160937702	MCF-7	breast:	n/a	n/a
4	REST	chr3:160937360-160937602	H1-hESC	embryonic stem cell:	n/a	n/a
5	REST	chr3:160937288-160937769	HL-60	blood:	n/a	n/a
6	REST	chr3:160937294-160937651	ECC-1	luminal epithelium:	n/a	n/a
7	REST	chr3:160937371-160937591	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160818503..160825890-chr3:160937051..160945986,18	MCF-7	breast:
2	chr3:160929000..160932392-chr3:160935549..160937889,3	K562	blood:
3	chr3:160934982..160947568-chr3:161079696..161093037,40	MCF-7	breast:
4	chr12:123319135..123321319-chr3:160936978..160939441,2	MCF-7	breast:
5	chr3:160936897..160938534-chr3:161143997..161146053,2	MCF-7	breast:
6	chr3:160936365..160960187-chr3:161078472..161094658,51	MCF-7	breast:
7	chr3:160936570..160938088-chr3:161064892..161066520,2	MCF-7	breast:
8	chr3:160919833..160921562-chr3:160936344..160938437,2	K562	blood:
9	chr3:160816932..160819441-chr3:160937058..160940131,3	MCF-7	breast:
10	chr3:160932923..160934841-chr3:160936654..160938320,2	K562	blood:
11	chr3:160821182..160827138-chr3:160937374..160941314,7	MCF-7	breast:

No data

Variant related genes	Relation type
NMD3	TF binding region
ENSG00000240567	Chromatin interaction
ENSG00000169251	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000169255	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1026572	0.82[CEU][hapmap]
rs10936223	0.90[AMR][1000 genomes]
rs10936224	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1154701	0.85[CEU][hapmap]
rs12486253	0.87[EUR][1000 genomes]
rs12495310	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12631850	0.90[AMR][1000 genomes]
rs13083229	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1478568	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs1599381	0.81[AMR][1000 genomes]
rs336580	0.84[CEU][hapmap]
rs4290817	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4470535	0.89[EUR][1000 genomes]
rs4518145	0.81[EUR][1000 genomes]
rs4560315	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4618258	0.83[AMR][1000 genomes]
rs462514	0.85[CEU][hapmap]
rs4856714	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4856738	0.89[EUR][1000 genomes]
rs4856767	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4856768	0.88[EUR][1000 genomes]
rs55688744	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6768818	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6770585	0.83[JPT][hapmap]
rs6774276	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs6789244	0.81[AMR][1000 genomes]
rs6789388	0.85[CEU][hapmap]
rs6791213	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6809256	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7611367	0.85[CEU][hapmap]
rs7613227	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7613358	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs7627528	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7630674	0.81[CEU][hapmap]
rs7630768	0.81[AMR][1000 genomes]
rs7632797	0.85[CEU][hapmap]
rs7633186	0.85[CEU][hapmap]
rs7636941	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7652267	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs899275	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9809522	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9815222	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9834659	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9839527	0.88[EUR][1000 genomes]
rs9871480	0.82[JPT][hapmap]
rs9879687	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9864752	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160926000-160938400	Weak transcription	Brain Substantia Nigra	brain
2	chr3:160931000-160938600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:160931800-160938400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:160933200-160939000	Weak transcription	Gastric	stomach
5	chr3:160933400-160938600	Weak transcription	Stomach Mucosa	stomach
6	chr3:160933600-160938400	Weak transcription	Fetal Intestine Large	intestine
7	chr3:160935600-160938000	Weak transcription	Hela-S3	cervix
8	chr3:160935600-160938400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:160935800-160938200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:160935800-160938200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:160935800-160938200	Weak transcription	HepG2	liver
12	chr3:160935800-160938200	Weak transcription	NHDF-Ad	bronchial
13	chr3:160935800-160938400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:160935800-160938600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:160936000-160938200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:160936000-160938200	Weak transcription	Osteobl	bone
17	chr3:160936000-160938400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:160936000-160938600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:160937000-160938400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:160937400-160938000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:160937400-160938800	Weak transcription	Aorta	Aorta

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