Variant report

Variant	rs9834659
Chromosome Location	chr3:160980947-160980948
allele	A/C
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:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:160980213..160981997-chr3:160984897..160987351,2	MCF-7	breast:
2	chr3:160980523..160999163-chr3:161073509..161094838,104	MCF-7	breast:
3	chr3:160980180..160982518-chr3:161034107..161036039,2	MCF-7	breast:
4	chr3:160977108..160997706-chr3:161077424..161093939,169	MCF-7	breast:
5	chr3:160962502..160964176-chr3:160980145..160982760,2	MCF-7	breast:
6	chr3:160977550..160980456-chr3:160980555..160982387,2	K562	blood:
7	chr3:160979328..160995719-chr3:161119748..161144811,174	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NMD3-2	chr3:160980940-160981507	NONHSAT093012

No data

Variant related genes	Relation type
ENSG00000240567	Chromatin interaction
ENSG00000196542	Chromatin interaction

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

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

rs_ID	r²[population]
rs10936223	0.88[AMR][1000 genomes]
rs10936224	0.91[AMR][1000 genomes]
rs1154701	0.89[EUR][1000 genomes]
rs12486253	0.98[EUR][1000 genomes]
rs12495310	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631850	0.88[AMR][1000 genomes]
rs13083229	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1478568	0.99[EUR][1000 genomes]
rs1599381	0.81[AMR][1000 genomes]
rs4290817	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4470535	1.00[EUR][1000 genomes]
rs4518145	0.87[EUR][1000 genomes]
rs4560315	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4618258	0.83[AMR][1000 genomes]
rs4856714	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4856738	1.00[EUR][1000 genomes]
rs4856739	0.90[EUR][1000 genomes]
rs4856767	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4856768	0.99[EUR][1000 genomes]
rs55688744	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6441370	0.89[EUR][1000 genomes]
rs6441371	0.87[EUR][1000 genomes]
rs6768818	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6774276	0.86[EUR][1000 genomes]
rs6789244	0.81[AMR][1000 genomes]
rs6789388	0.90[EUR][1000 genomes]
rs6791213	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6809256	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7611367	0.89[EUR][1000 genomes]
rs7613227	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7613358	0.98[EUR][1000 genomes]
rs7615592	0.81[EUR][1000 genomes]
rs7623206	0.81[EUR][1000 genomes]
rs7627528	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7630768	0.81[AMR][1000 genomes]
rs7632797	0.89[EUR][1000 genomes]
rs7633186	0.88[EUR][1000 genomes]
rs7636941	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7652267	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs899275	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9809522	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815222	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9839527	0.99[EUR][1000 genomes]
rs9846756	0.80[EUR][1000 genomes]
rs9864752	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9879687	0.88[AMR][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
rs9834659	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160939800-160995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:160941000-160983000	Weak transcription	Spleen	Spleen
3	chr3:160941000-160984600	Weak transcription	Small Intestine	intestine
4	chr3:160941000-160993400	Weak transcription	Pancreas	Pancrea
5	chr3:160956400-160993000	Weak transcription	Esophagus	oesophagus
6	chr3:160958600-160983600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:160966200-160983400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:160966200-160987400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:160966200-160993200	Weak transcription	Right Ventricle	heart
10	chr3:160966400-160982000	Weak transcription	Fetal Intestine Small	intestine
11	chr3:160968800-160992200	Weak transcription	Brain Angular Gyrus	brain
12	chr3:160970200-160983800	Weak transcription	NHLF	lung
13	chr3:160970400-160984200	Weak transcription	Hela-S3	cervix
14	chr3:160970400-160995600	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:160970800-160981800	Weak transcription	Lung	lung
16	chr3:160970800-160982200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:160970800-160995600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:160971000-160981000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr3:160971000-160981800	Weak transcription	Ovary	ovary
20	chr3:160971000-160982200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr3:160971000-160983600	Weak transcription	Thymus	Thymus
22	chr3:160971000-160984200	Weak transcription	Brain Anterior Caudate	brain
23	chr3:160971000-160987400	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:160971000-160989000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:160971000-160993800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr3:160971000-160995400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:160971000-160995400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:160971200-160982000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:160971200-160984400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:160971200-160988800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:160971200-160995200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:160971200-160996000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:160971400-160982000	Weak transcription	HepG2	liver
34	chr3:160971600-160982000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:160971800-160993000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:160972200-160996600	Weak transcription	Brain Substantia Nigra	brain
37	chr3:160972400-160993800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr3:160972600-160984400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:160972800-160995400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr3:160973000-160984000	Weak transcription	Stomach Mucosa	stomach
41	chr3:160973200-160982000	Weak transcription	Aorta	Aorta
42	chr3:160973200-160983800	Weak transcription	K562	blood
43	chr3:160973200-160984600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr3:160973200-160993200	Weak transcription	Gastric	stomach
45	chr3:160973400-160989000	Weak transcription	Fetal Thymus	thymus
46	chr3:160973600-160981000	Weak transcription	Fetal Heart	heart
47	chr3:160974000-160983000	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr3:160974600-160990000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr3:160975200-160981600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr3:160975200-160982000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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