Variant report

Variant	rs1317320
Chromosome Location	chr15:77830090-77830091
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77828874..77831053-chr15:77833422..77835199,2	MCF-7	breast:
2	chr15:77829651..77831982-chr15:77834371..77837022,2	MCF-7	breast:
3	chr15:77827126..77831240-chr15:77834209..77836612,4	K562	blood:
4	chr1:1179419..1181281-chr15:77828789..77830310,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184163	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11855272	0.85[ASN][1000 genomes]
rs16968893	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16968895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16968897	0.92[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs16968900	0.81[ASN][1000 genomes]
rs16968930	0.89[JPT][hapmap]
rs17394448	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2137111	0.89[JPT][hapmap]
rs2867303	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4243046	0.85[ASN][1000 genomes]
rs4886870	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886874	0.89[JPT][hapmap];0.86[MEX][hapmap]
rs74026930	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74026931	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74026932	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74026933	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7495653	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs869302	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs869310	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs907371	0.89[JPT][hapmap];0.82[MEX][hapmap]
rs907387	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1043284	chr15:77740632-77884026	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv570139	chr15:77762493-77865459	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv570140	chr15:77787469-77851535	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1317320	TSPAN3	cis	Whole Blood	GTEx
rs1317320	C15orf60	cis	parietal	SCAN
rs1317320	Contig47326	trans	multi-tissue	Pritchard
rs1317320	TSPAN3	cis	cerebellum	SCAN
rs1317320	C15orf5	cis	cerebellum	SCAN
rs1317320	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL
rs1317320	C1orf228	cis	Liver	GTEx
rs1317320	AL109670	cis	multi-tissue	Pritchard
rs1317320	HMG20A	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77819800-77831000	Weak transcription	Gastric	stomach
2	chr15:77821000-77831200	Weak transcription	Esophagus	oesophagus
3	chr15:77821600-77830200	Weak transcription	Left Ventricle	heart
4	chr15:77822000-77833600	Weak transcription	Right Atrium	heart
5	chr15:77825800-77830200	Weak transcription	Right Ventricle	heart
6	chr15:77825800-77831000	Weak transcription	Stomach Mucosa	stomach
7	chr15:77827000-77833200	Weak transcription	HSMMtube	muscle
8	chr15:77827000-77835400	Weak transcription	Psoas Muscle	Psoas
9	chr15:77827000-77845400	Weak transcription	Fetal Kidney	kidney
10	chr15:77827200-77830200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr15:77827600-77832400	Enhancers	Pancreas	Pancrea
12	chr15:77827600-77834000	Enhancers	Primary B cells from peripheral blood	blood
13	chr15:77827800-77831200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr15:77828400-77831400	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr15:77828400-77831800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr15:77828400-77831800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr15:77828400-77832000	Enhancers	Brain Hippocampus Middle	brain
18	chr15:77828400-77832400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr15:77828400-77833400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr15:77828400-77835400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:77828400-77835400	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr15:77828400-77835400	Enhancers	Brain Anterior Caudate	brain
23	chr15:77828600-77830200	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr15:77828600-77831200	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr15:77828600-77831400	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr15:77828600-77831600	Enhancers	H9 Cell Line	embryonic stem cell
27	chr15:77828600-77831600	Enhancers	Brain Germinal Matrix	brain
28	chr15:77828600-77831800	Enhancers	H1 Cell Line	embryonic stem cell
29	chr15:77828600-77832000	Enhancers	Brain Angular Gyrus	brain
30	chr15:77828600-77832000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:77828600-77833200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:77828600-77834000	Enhancers	Primary B cells from cord blood	blood
33	chr15:77828600-77834200	Enhancers	Brain Substantia Nigra	brain
34	chr15:77828800-77831400	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr15:77828800-77831600	Weak transcription	Placenta	Placenta
36	chr15:77828800-77832200	Enhancers	Brain Cingulate Gyrus	brain
37	chr15:77828800-77833400	Weak transcription	K562	blood
38	chr15:77829000-77831200	Weak transcription	Fetal Heart	heart
39	chr15:77829000-77831200	Enhancers	Spleen	Spleen
40	chr15:77829000-77831800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr15:77829000-77833000	Weak transcription	Fetal Intestine Large	intestine
42	chr15:77829200-77830800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr15:77829400-77831200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr15:77829400-77831400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr15:77829400-77831400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:77829400-77835000	Enhancers	Fetal Muscle Trunk	muscle
47	chr15:77829400-77844800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:77829600-77831600	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr15:77829600-77835400	Enhancers	Fetal Stomach	stomach
50	chr15:77829800-77830200	Weak transcription	Fetal Intestine Small	intestine

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