Variant report

Variant	rs4310476
Chromosome Location	chr1:153663447-153663448
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153662725..153665367-chr1:153669060..153670825,2	MCF-7	breast:
2	chr1:153651210..153654277-chr1:153662506..153664401,3	K562	blood:
3	chr1:153648759..153654433-chr1:153661567..153666509,7	K562	blood:

Variant related genes	Relation type
ENSG00000169418	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10797096	0.82[AMR][1000 genomes]
rs10908848	0.84[AMR][1000 genomes]
rs11265625	0.84[AMR][1000 genomes]
rs11588347	0.82[AMR][1000 genomes]
rs4845564	0.82[AMR][1000 genomes]
rs55772653	0.84[AMR][1000 genomes]
rs6674929	0.82[AMR][1000 genomes]
rs9662664	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv547928	chr1:153612133-153714252	Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv2830411	chr1:153613393-153725007	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv1067771	chr1:153613593-153724866	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv530052	chr1:153613593-153724866	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv1005818	chr1:153613597-153724980	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv535173	chr1:153613597-153724980	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv1007835	chr1:153613597-153729959	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv535174	chr1:153613597-153729959	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
11	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
12	nsv464028	chr1:153622220-153723037	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv547929	chr1:153622220-153723037	Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
15	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
16	nsv1001312	chr1:153622834-153724867	Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv535176	chr1:153622834-153724867	Active TSS Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4310476	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs4310476	S100A13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153652400-153664600	Weak transcription	Gastric	stomach
2	chr1:153652400-153669800	Weak transcription	Pancreas	Pancrea
3	chr1:153653000-153669800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:153653200-153664000	Weak transcription	Left Ventricle	heart
5	chr1:153653200-153669800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:153653800-153666400	Strong transcription	Lung	lung
7	chr1:153653800-153669400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:153654400-153669200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:153654400-153669400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:153655400-153669800	Weak transcription	Esophagus	oesophagus
11	chr1:153656600-153669400	Weak transcription	Fetal Kidney	kidney
12	chr1:153656800-153666400	Strong transcription	Aorta	Aorta
13	chr1:153656800-153669200	Weak transcription	A549	lung
14	chr1:153657400-153664000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:153658200-153669600	Weak transcription	Right Atrium	heart
16	chr1:153658400-153669600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:153659800-153669800	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:153660000-153669400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:153660000-153669600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:153660000-153670200	Weak transcription	Fetal Intestine Small	intestine
21	chr1:153660600-153669400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:153661000-153663800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:153661000-153666600	Strong transcription	Adipose Nuclei	Adipose
24	chr1:153661000-153669400	Weak transcription	K562	blood
25	chr1:153661000-153669600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:153661800-153670600	Weak transcription	Colonic Mucosa	Colon
27	chr1:153662200-153665400	Weak transcription	Hela-S3	cervix
28	chr1:153662200-153669600	Weak transcription	Placenta	Placenta
29	chr1:153662200-153669600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr1:153662200-153670000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:153662400-153666000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:153662400-153669600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr1:153662800-153663800	Enhancers	Primary T cells fromperipheralblood	blood
34	chr1:153662800-153663800	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr1:153662800-153663800	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr1:153662800-153669600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:153662800-153669600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:153663000-153664000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr1:153663000-153665600	Weak transcription	Right Ventricle	heart
40	chr1:153663000-153669400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr1:153663200-153663600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr1:153663200-153664000	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr1:153663200-153665600	Weak transcription	Ovary	ovary
44	chr1:153663400-153664000	Enhancers	Fetal Thymus	thymus
45	chr1:153663400-153669600	Weak transcription	Fetal Stomach	stomach

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