Variant report

Variant	rs4470535
Chromosome Location	chr3:160974468-160974469
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160966019..160968208-chr3:160972559..160974651,2	MCF-7	breast:
2	chr3:160973929..160975707-chr3:161135693..161137534,2	MCF-7	breast:
3	chr3:160971520..160973570-chr3:160974078..160977165,3	MCF-7	breast:
4	chr3:160973015..160975782-chr3:160983257..160984865,2	MCF-7	breast:
5	chr3:160974298..160976204-chr3:161090106..161091983,2	MCF-7	breast:
6	chr3:160968713..160970320-chr3:160973701..160975272,2	MCF-7	breast:
7	chr3:160971821..160974643-chr3:161089062..161091131,3	MCF-7	breast:
8	chr3:160970413..160971945-chr3:160972168..160974529,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1026572	0.86[AMR][1000 genomes]
rs1154701	0.89[EUR][1000 genomes]
rs12486253	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12495310	1.00[EUR][1000 genomes]
rs13083229	0.98[EUR][1000 genomes]
rs1478568	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4290817	0.98[EUR][1000 genomes]
rs4518145	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4560315	1.00[EUR][1000 genomes]
rs4856714	0.99[EUR][1000 genomes]
rs4856738	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4856739	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4856767	0.99[EUR][1000 genomes]
rs4856768	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55688744	0.96[EUR][1000 genomes]
rs6441370	0.89[EUR][1000 genomes]
rs6441371	0.87[EUR][1000 genomes]
rs6768818	0.98[EUR][1000 genomes]
rs6774276	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6778254	0.86[AMR][1000 genomes]
rs6789388	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6791213	0.94[EUR][1000 genomes]
rs6809256	0.95[EUR][1000 genomes]
rs73875458	0.81[ASN][1000 genomes]
rs7611367	0.89[EUR][1000 genomes]
rs7613227	0.94[EUR][1000 genomes]
rs7613358	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7615592	0.81[EUR][1000 genomes]
rs7623206	0.81[EUR][1000 genomes]
rs7627528	0.98[EUR][1000 genomes]
rs7632797	0.89[EUR][1000 genomes]
rs7633186	0.88[EUR][1000 genomes]
rs7636941	0.97[EUR][1000 genomes]
rs7652267	0.97[EUR][1000 genomes]
rs899275	0.94[EUR][1000 genomes]
rs9290069	0.88[AMR][1000 genomes]
rs9809522	1.00[EUR][1000 genomes]
rs9815222	0.99[EUR][1000 genomes]
rs9834659	1.00[EUR][1000 genomes]
rs9839527	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9846756	0.80[EUR][1000 genomes]
rs9864752	0.89[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4470535	SPTSSB	cis	Heart Left Ventricle	GTEx
rs4470535	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 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	chr3:160940000-160977400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:160941000-160974800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:160941000-160983000	Weak transcription	Spleen	Spleen
5	chr3:160941000-160984600	Weak transcription	Small Intestine	intestine
6	chr3:160941000-160993400	Weak transcription	Pancreas	Pancrea
7	chr3:160941600-160975400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:160941800-160975200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr3:160942400-160975200	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr3:160942600-160975000	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:160942600-160976600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:160942800-160978000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:160943600-160977200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:160948800-160978000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:160950000-160978000	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:160950200-160976600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:160951000-160976600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:160951400-160975200	Strong transcription	Osteobl	bone
19	chr3:160951600-160975000	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr3:160951600-160976600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:160955000-160975400	Strong transcription	Fetal Intestine Large	intestine
22	chr3:160955800-160974600	Strong transcription	Duodenum Mucosa	Duodenum
23	chr3:160956400-160993000	Weak transcription	Esophagus	oesophagus
24	chr3:160958600-160983600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:160964200-160976600	Strong transcription	Adipose Nuclei	Adipose
26	chr3:160964200-160978600	Strong transcription	A549	lung
27	chr3:160964400-160978200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:160965200-160976800	Strong transcription	Liver	Liver
29	chr3:160966200-160980800	Weak transcription	Fetal Stomach	stomach
30	chr3:160966200-160983400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:160966200-160987400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:160966200-160993200	Weak transcription	Right Ventricle	heart
33	chr3:160966400-160982000	Weak transcription	Fetal Intestine Small	intestine
34	chr3:160967200-160975800	Weak transcription	Colonic Mucosa	Colon
35	chr3:160968800-160992200	Weak transcription	Brain Angular Gyrus	brain
36	chr3:160970200-160979000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:160970200-160980800	Weak transcription	NHEK	skin
38	chr3:160970200-160983800	Weak transcription	NHLF	lung
39	chr3:160970400-160976000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr3:160970400-160980600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr3:160970400-160984200	Weak transcription	Hela-S3	cervix
42	chr3:160970400-160995600	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:160970600-160975800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr3:160970800-160974600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:160970800-160981800	Weak transcription	Lung	lung
46	chr3:160970800-160982200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr3:160970800-160995600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:160971000-160975400	Weak transcription	Fetal Lung	lung
49	chr3:160971000-160981000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr3:160971000-160981800	Weak transcription	Ovary	ovary

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