Variant report

Variant	rs7664717
Chromosome Location	chr4:88289342-88289343
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:88288892..88291753-chr4:88294244..88297136,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198189	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11097131	0.88[EUR][1000 genomes]
rs11097147	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11721653	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11726577	0.81[EUR][1000 genomes]
rs11734330	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11737402	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11930147	0.88[EUR][1000 genomes]
rs11930151	0.88[EUR][1000 genomes]
rs11939415	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11946007	0.88[EUR][1000 genomes]
rs12505484	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55895035	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932175	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56141705	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56258452	0.88[EUR][1000 genomes]
rs56284919	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56385009	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56390566	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56788263	0.88[EUR][1000 genomes]
rs58360495	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60597105	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305726	0.86[EUR][1000 genomes]
rs62305728	0.88[EUR][1000 genomes]
rs62305729	0.88[EUR][1000 genomes]
rs62305730	0.86[EUR][1000 genomes]
rs62305731	0.88[EUR][1000 genomes]
rs62305732	0.88[EUR][1000 genomes]
rs62305753	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62319084	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62319094	1.00[ASN][1000 genomes]
rs72652029	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7665549	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7671557	0.81[EUR][1000 genomes]
rs7674658	0.81[EUR][1000 genomes]
rs7690170	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870296	chr4:88173534-88295927	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7664717	HSD17B13	cis	Nerve Tibial	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88254800-88311800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:88255000-88292400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:88255200-88293800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:88256200-88292800	Weak transcription	Gastric	stomach
5	chr4:88256200-88310600	Weak transcription	Right Ventricle	heart
6	chr4:88257000-88291000	Weak transcription	HUVEC	blood vessel
7	chr4:88257800-88311800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:88266400-88292200	Weak transcription	Fetal Brain Male	brain
9	chr4:88267400-88290600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr4:88267400-88308000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr4:88267600-88292400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:88267800-88306000	Weak transcription	Fetal Brain Female	brain
13	chr4:88268000-88292200	Weak transcription	Ovary	ovary
14	chr4:88271200-88298000	Weak transcription	HSMMtube	muscle
15	chr4:88273000-88292200	Weak transcription	Brain Substantia Nigra	brain
16	chr4:88273400-88298800	Weak transcription	Fetal Heart	heart
17	chr4:88274200-88296200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr4:88274400-88296400	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr4:88274400-88297000	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr4:88274400-88303400	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr4:88274600-88296200	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr4:88274600-88296400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr4:88274600-88296600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr4:88274600-88297200	Strong transcription	Fetal Intestine Large	intestine
25	chr4:88274800-88296400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr4:88274800-88298200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr4:88275200-88292200	Weak transcription	Brain Hippocampus Middle	brain
28	chr4:88275200-88292400	Weak transcription	GM12878-XiMat	blood
29	chr4:88275200-88296200	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr4:88275200-88299400	Strong transcription	Dnd41	blood
31	chr4:88276000-88292400	Weak transcription	NHDF-Ad	bronchial
32	chr4:88276200-88292400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr4:88276200-88292600	Weak transcription	NHLF	lung
34	chr4:88276200-88296000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr4:88276200-88311400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:88276400-88292200	Weak transcription	Osteobl	bone
37	chr4:88276400-88292400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:88276400-88295800	Weak transcription	HMEC	breast
39	chr4:88276400-88302800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:88277000-88292400	Weak transcription	Brain Anterior Caudate	brain
41	chr4:88278000-88295800	Strong transcription	Primary B cells from peripheral blood	blood
42	chr4:88278200-88292800	Weak transcription	Esophagus	oesophagus
43	chr4:88278400-88292400	Weak transcription	HSMM	muscle
44	chr4:88278600-88292600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr4:88278600-88292600	Weak transcription	Stomach Mucosa	stomach
46	chr4:88278800-88292400	Weak transcription	Brain Angular Gyrus	brain
47	chr4:88278800-88297200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr4:88279800-88297200	Strong transcription	Duodenum Mucosa	Duodenum
49	chr4:88280200-88296400	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr4:88280400-88289400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links