Variant report

Variant	rs7617204
Chromosome Location	chr3:160821969-160821970
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr3:160821640-160823909	MCF-7	breast:	n/a	n/a
2	HDAC2	chr3:160821953-160823716	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:160818503..160825890-chr3:160937051..160945986,18	MCF-7	breast:
2	chr3:160819969..160822199-chr3:161125222..161127254,2	MCF-7	breast:
3	chr3:160821182..160827138-chr3:160937374..160941314,7	MCF-7	breast:
4	chr3:160813033..160824577-chr3:161083489..161092050,35	MCF-7	breast:

Variant related genes	Relation type
B3GALNT1	TF binding region
NMD3	TF binding region
ENSG00000196542	Chromatin interaction
ENSG00000271052	Chromatin interaction
ENSG00000169251	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1026572	0.94[EUR][1000 genomes]
rs10936223	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12493960	0.82[EUR][1000 genomes]
rs12631850	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13066683	0.91[EUR][1000 genomes]
rs1599374	0.82[EUR][1000 genomes]
rs1599376	0.82[EUR][1000 genomes]
rs1599378	0.86[EUR][1000 genomes]
rs1599379	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1599381	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1599383	0.91[EUR][1000 genomes]
rs1599386	0.90[EUR][1000 genomes]
rs1599389	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1599390	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1609688	0.85[EUR][1000 genomes]
rs1610158	0.91[EUR][1000 genomes]
rs2306061	0.81[EUR][1000 genomes]
rs4342141	0.89[EUR][1000 genomes]
rs4557202	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4616689	0.89[EUR][1000 genomes]
rs4618258	0.86[EUR][1000 genomes]
rs6441354	1.00[EUR][1000 genomes]
rs6765270	0.83[EUR][1000 genomes]
rs6774635	0.90[EUR][1000 genomes]
rs6778254	0.91[EUR][1000 genomes]
rs6783085	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6789244	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6799130	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7614375	1.00[EUR][1000 genomes]
rs7619011	0.91[EUR][1000 genomes]
rs7625363	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7630768	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7633857	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7637086	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7647285	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7650703	0.90[EUR][1000 genomes]
rs7651087	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9290069	0.91[EUR][1000 genomes]
rs9820825	0.91[EUR][1000 genomes]
rs9848239	0.90[EUR][1000 genomes]
rs9867582	0.96[EUR][1000 genomes]
rs9879687	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv877704	chr3:160806859-160836006	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv877705	chr3:160818188-160836006	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv877706	chr3:160820175-160826404	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv877707	chr3:160820175-160836006	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3420135	chr3:160821883-160824431	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv877708	chr3:160821969-160826404	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7617204	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160781800-160822000	Weak transcription	Thymus	Thymus
2	chr3:160787000-160822000	Weak transcription	Primary T cells from cord blood	blood
3	chr3:160797000-160822000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:160799800-160822000	Weak transcription	HMEC	breast
5	chr3:160800400-160822200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:160800400-160822400	Weak transcription	Spleen	Spleen
7	chr3:160801200-160822000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:160802600-160822000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:160802600-160822400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:160802800-160822000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:160803400-160822000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:160803800-160822000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:160804400-160822000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:160804400-160822000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:160804600-160822200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:160809000-160822200	Weak transcription	Psoas Muscle	Psoas
17	chr3:160813400-160822000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:160816000-160822200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:160817200-160822000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr3:160817400-160822000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:160817800-160822000	Weak transcription	NHEK	skin
22	chr3:160818800-160822000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:160819000-160822200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:160819400-160822000	Weak transcription	Adipose Nuclei	Adipose
25	chr3:160819400-160822000	Weak transcription	Liver	Liver
26	chr3:160819400-160822000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:160819400-160822000	Weak transcription	Esophagus	oesophagus
28	chr3:160819400-160822000	Weak transcription	Right Atrium	heart
29	chr3:160819400-160822200	Weak transcription	Gastric	stomach
30	chr3:160820000-160822000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr3:160820000-160822000	Weak transcription	Fetal Intestine Large	intestine
32	chr3:160820000-160822200	Weak transcription	Placenta	Placenta
33	chr3:160820200-160822000	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:160820600-160822000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr3:160820600-160822000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:160820600-160822000	Weak transcription	Aorta	Aorta
37	chr3:160820800-160822000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:160820800-160822000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:160820800-160822000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:160820800-160822000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:160820800-160822000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:160820800-160822000	Weak transcription	Ovary	ovary
43	chr3:160821000-160822000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:160821200-160822000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr3:160821400-160822000	Enhancers	Fetal Brain Male	brain
46	chr3:160821400-160822200	Flanking Active TSS	Fetal Heart	heart
47	chr3:160821600-160822000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:160821600-160822000	Enhancers	Fetal Intestine Small	intestine
49	chr3:160821600-160822200	Enhancers	Pancreas	Pancrea
50	chr3:160821600-160823200	Active TSS	Right Ventricle	heart

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