Variant report

Variant	rs1503813
Chromosome Location	chr1:161700679-161700680
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	JUND	chr1:161699648-161700687	HCT-116	colon:	n/a	chr1:161700217-161700225 chr1:161699958-161699968 chr1:161700217-161700224
2	GATA3	chr1:161699862-161700691	SK-N-SH	brain:	n/a	chr1:161699952-161699962
3	GATA3	chr1:161699816-161700711	SK-N-SH	brain:	n/a	chr1:161699952-161699962
4	SP1	chr1:161699646-161701157	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
RN7SL466P	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11810305	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12408296	0.80[CHB][hapmap]
rs1503812	1.00[ASN][1000 genomes]
rs2840310	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4657093	0.81[CHB][hapmap]
rs6698889	0.89[ASN][1000 genomes]
rs905589	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[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	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv516773	chr1:161691433-161702763	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	n/a
6	nsv464195	chr1:161693003-161702792	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a
7	nsv548076	chr1:161693003-161702792	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1503813	PVRL4	cis	cerebellum	SCAN
rs1503813	FCRLA	cis	lymphoblastoid	seeQTL
rs1503813	ATF6	cis	parietal	SCAN
rs1503813	PYHIN1	cis	cerebellum	SCAN
rs1503813	F11R	cis	cerebellum	SCAN
rs1503813	C1orf226	cis	lymphoblastoid	seeQTL
rs1503813	FCRLB	cis	multi-tissue	Pritchard

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161697600-161700800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:161697600-161700800	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr1:161697600-161700800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:161697800-161700800	Enhancers	Primary T cells fromperipheralblood	blood
5	chr1:161697800-161700800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:161697800-161700800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:161697800-161700800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr1:161697800-161706600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:161698000-161702600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:161698000-161703400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:161698000-161703400	Enhancers	K562	blood
12	chr1:161698000-161706000	Enhancers	NHEK	skin
13	chr1:161698000-161707600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:161698400-161704400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:161698600-161700800	Enhancers	NHDF-Ad	bronchial
16	chr1:161698600-161705600	Weak transcription	A549	lung
17	chr1:161698800-161702600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:161699200-161704400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:161699200-161707400	Enhancers	HMEC	breast
20	chr1:161699400-161700800	Enhancers	HUVEC	blood vessel
21	chr1:161699600-161700800	Enhancers	Hela-S3	cervix
22	chr1:161699800-161700800	Enhancers	Muscle Satellite Cultured Cells	--
23	chr1:161700000-161700800	Enhancers	Osteobl	bone
24	chr1:161700000-161701400	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr1:161700000-161701800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:161700000-161702200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:161700200-161700800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:161700200-161707800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr1:161700200-161708400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:161700400-161700800	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr1:161700400-161700800	Enhancers	GM12878-XiMat	blood
32	chr1:161700400-161701000	Enhancers	H9 Cell Line	embryonic stem cell
33	chr1:161700600-161700800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:161700600-161700800	Enhancers	NH-A	brain
35	chr1:161700600-161702600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:161700600-161702800	Weak transcription	HSMM	muscle
37	chr1:161700600-161702800	Weak transcription	NHLF	lung
38	chr1:161700600-161703000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:161700600-161703000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:161700600-161705400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:161700600-161705600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:161700600-161706000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:161700600-161706200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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