Variant report

Variant	rs480108
Chromosome Location	chr15:43817406-43817407
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:43812804..43815788-chr15:43816222..43819010,3	K562	blood:
2	chr15:43809318..43812744-chr15:43815463..43818743,6	K562	blood:
3	chr15:43806460..43809069-chr15:43815208..43818201,3	K562	blood:
4	chr15:43814200..43815983-chr15:43816527..43818249,2	MCF-7	breast:
5	chr15:43806714..43809115-chr15:43817387..43820245,2	MCF-7	breast:
6	chr1:59250077..59250595-chr15:43817366..43818272,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000166963	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1060939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1079309	0.91[CEU][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12905772	0.84[CEU][hapmap]
rs1814538	0.95[JPT][hapmap]
rs1869258	1.00[CEU][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2242069	0.95[JPT][hapmap]
rs2244981	0.91[CEU][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2245715	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2249952	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2250750	0.81[AMR][1000 genomes]
rs2251844	0.97[ASN][1000 genomes]
rs2253268	0.91[CEU][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2253708	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2254927	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2255042	0.99[ASN][1000 genomes]
rs2255051	0.94[ASN][1000 genomes]
rs2255410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2255663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2264050	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2264876	0.91[JPT][hapmap]
rs2278857	0.87[CEU][hapmap]
rs2412781	0.91[CEU][hapmap]
rs2439831	0.95[JPT][hapmap]
rs2439832	0.95[JPT][hapmap]
rs2439834	0.89[ASN][1000 genomes]
rs2439839	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2439843	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2439845	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2439846	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2439850	0.91[JPT][hapmap]
rs2444032	0.95[JPT][hapmap]
rs2444244	0.94[ASN][1000 genomes]
rs2444250	0.91[JPT][hapmap]
rs2444251	0.91[CEU][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2467736	0.95[JPT][hapmap]
rs2467737	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2467738	0.87[CEU][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2467739	0.95[JPT][hapmap]
rs2467741	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2467742	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2467745	0.91[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470130	0.99[ASN][1000 genomes]
rs2470131	0.99[ASN][1000 genomes]
rs2584725	0.80[ASN][1000 genomes]
rs2602141	0.91[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28649346	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28758851	0.80[AMR][1000 genomes]
rs2915788	0.94[ASN][1000 genomes]
rs2924369	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2927070	0.82[AMR][1000 genomes]
rs2927071	0.80[AMR][1000 genomes]
rs3097773	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs3809482	0.91[CEU][hapmap]
rs4296223	0.91[CEU][hapmap]
rs4547312	0.87[CEU][hapmap]
rs475486	0.92[ASN][1000 genomes]
rs486301	0.97[ASN][1000 genomes]
rs493377	0.91[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs495175	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs496584	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs499035	0.84[AFR][1000 genomes]
rs506120	0.91[CEU][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs509306	0.80[EUR][1000 genomes]
rs510108	0.84[AFR][1000 genomes]
rs518288	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs523156	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs529611	1.00[CEU][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs536313	0.91[CEU][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs537115	0.95[JPT][hapmap]
rs542898	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs548704	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs560191	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs570933	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs572837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs576557	0.84[AFR][1000 genomes]
rs6493083	0.91[CEU][hapmap]
rs689647	0.95[JPT][hapmap]
rs689693	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs689767	0.88[CEU][hapmap];0.91[JPT][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs689781	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs689797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689826	0.91[JPT][hapmap]
rs689835	0.91[JPT][hapmap]
rs689883	0.99[ASN][1000 genomes]
rs690012	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs690276	0.91[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes]
rs690316	0.91[JPT][hapmap]
rs690367	0.91[CEU][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs690436	0.95[JPT][hapmap]
rs690446	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs690466	0.91[JPT][hapmap]
rs690472	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs690512	0.88[CEU][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes]
rs693510	0.88[CEU][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs694725	0.91[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs694985	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7163288	0.91[CEU][hapmap]
rs7167882	0.80[AMR][1000 genomes]
rs7497780	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9920879	0.91[CEU][hapmap]

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	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv437799	chr15:43784000-43989518	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv515877	chr15:43802024-43818052	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv518707	chr15:43802024-43826557	Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
7	nsv832988	chr15:43804641-43976862	Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs480108	TGM7	cis	Esophagus Mucosa	GTEx
rs480108	TGM5	cis	multi-tissue	Pritchard
rs480108	STRCP1	cis	Esophagus Muscularis	GTEx
rs480108	STRCP1	cis	Whole Blood	GTEx
rs480108	ZSCAN29	cis	multi-tissue	Pritchard
rs480108	AC011330.5	cis	Artery Tibial	GTEx
rs480108	ZSCAN29	cis	Thyroid	GTEx
rs480108	AC011330.5	cis	Thyroid	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43810400-43826200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:43810600-43826400	Weak transcription	Spleen	Spleen
3	chr15:43810800-43817600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr15:43810800-43824000	Weak transcription	Fetal Kidney	kidney
5	chr15:43810800-43826000	Weak transcription	Esophagus	oesophagus
6	chr15:43811000-43818600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr15:43811000-43828600	Weak transcription	Pancreas	Pancrea
8	chr15:43811200-43820600	Weak transcription	Colonic Mucosa	Colon
9	chr15:43811200-43823600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:43811200-43826800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr15:43811400-43829200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:43812000-43823200	Strong transcription	Stomach Smooth Muscle	stomach
13	chr15:43812000-43844400	Weak transcription	Fetal Brain Male	brain
14	chr15:43812200-43818000	Strong transcription	Fetal Intestine Large	intestine
15	chr15:43812200-43819000	Strong transcription	Osteobl	bone
16	chr15:43812200-43823200	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr15:43812200-43823800	Strong transcription	NHLF	lung
18	chr15:43812400-43817800	ZNF genes & repeats	Aorta	Aorta
19	chr15:43812400-43818200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr15:43812400-43819000	ZNF genes & repeats	Fetal Stomach	stomach
21	chr15:43812400-43821400	Strong transcription	HSMMtube	muscle
22	chr15:43812400-43823200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:43812600-43817600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr15:43812600-43817800	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr15:43812600-43818200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr15:43812600-43818200	Strong transcription	Left Ventricle	heart
27	chr15:43812600-43818800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:43812600-43819600	Strong transcription	HSMM	muscle
29	chr15:43812600-43819600	Strong transcription	NH-A	brain
30	chr15:43812600-43820000	Genic enhancers	Brain Hippocampus Middle	brain
31	chr15:43812600-43820400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:43812600-43823200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr15:43812600-43823200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:43812800-43817600	Strong transcription	Fetal Lung	lung
35	chr15:43812800-43818000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr15:43812800-43818000	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr15:43812800-43818200	Strong transcription	Colon Smooth Muscle	Colon
38	chr15:43812800-43818800	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr15:43812800-43819800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:43812800-43820200	Strong transcription	NHDF-Ad	bronchial
41	chr15:43812800-43822400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr15:43812800-43823200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr15:43812800-43823800	Strong transcription	Brain Germinal Matrix	brain
44	chr15:43812800-43824200	Strong transcription	Fetal Brain Female	brain
45	chr15:43813200-43818200	ZNF genes & repeats	Fetal Muscle Leg	muscle
46	chr15:43813200-43819200	Strong transcription	Right Ventricle	heart
47	chr15:43813400-43818000	Strong transcription	Rectal Smooth Muscle	rectum
48	chr15:43813600-43817800	Strong transcription	Adipose Nuclei	Adipose
49	chr15:43813600-43823400	Strong transcription	Fetal Intestine Small	intestine
50	chr15:43813800-43820000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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