Variant report

Variant	rs905589
Chromosome Location	chr1:161703198-161703199
allele	C/T
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	FOS	chr1:161703074-161703759	MCF10A-Er-Src	breast:	n/a	chr1:161703544-161703555
2	EP300	chr1:161703197-161703834	SK-N-SH	brain:	n/a	chr1:161703787-161703797
3	STAT3	chr1:161703139-161703776	MCF10A-Er-Src	breast:	n/a	n/a
4	FOSL1	chr1:161703163-161703858	HCT-116	colon:	n/a	n/a
5	CEBPB	chr1:161703188-161703891	HCT-116	colon:	n/a	n/a
6	FOSL2	chr1:161703163-161703820	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr1:161703196-161703748	SK-N-SH	brain:	n/a	n/a
8	FOS	chr1:161703133-161703750	MCF10A-Er-Src	breast:	n/a	chr1:161703544-161703555

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:161702286..161705058-chr1:161705873..161710501,6	K562	blood:

Variant related genes	Relation type
RN7SL466P	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs11576107	0.85[TSI][hapmap]
rs11810305	0.98[ASN][1000 genomes]
rs12408296	0.80[CHB][hapmap]
rs1503812	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503813	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2840310	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657093	0.81[CHB][hapmap]
rs6698889	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv527196	chr1:161703018-161703198	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs905589	C1orf226	cis	lymphoblastoid	seeQTL
rs905589	FCGR2A	cis	parietal	SCAN
rs905589	FCRLA	cis	lymphoblastoid	seeQTL
rs905589	FCRLA	cis	multi-tissue	Pritchard
rs905589	FCRLA	Cis_1M	lymphoblastoid	RTeQTL
rs905589	DDR2	cis	cerebellum	SCAN
rs905589	FCGR2B	cis	multi-tissue	Pritchard
rs905589	ATF6	cis	parietal	SCAN
rs905589	FCRLM2	cis	multi-tissue	Pritchard

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161697800-161706600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:161698000-161703400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr1:161698000-161703400	Enhancers	K562	blood
4	chr1:161698000-161706000	Enhancers	NHEK	skin
5	chr1:161698000-161707600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:161698400-161704400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:161698600-161705600	Weak transcription	A549	lung
8	chr1:161699200-161704400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:161699200-161707400	Enhancers	HMEC	breast
10	chr1:161700200-161707800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr1:161700200-161708400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr1:161700600-161705400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:161700600-161705600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:161700600-161706000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:161700600-161706200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:161700800-161705000	Weak transcription	GM12878-XiMat	blood
17	chr1:161700800-161705600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:161700800-161706000	Weak transcription	Hela-S3	cervix
19	chr1:161701000-161706000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:161701400-161704000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:161701400-161706000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:161701800-161705600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:161702200-161703200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:161702600-161703200	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr1:161702600-161704400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:161702600-161704400	Enhancers	Muscle Satellite Cultured Cells	--
27	chr1:161702600-161704600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:161702600-161704600	Enhancers	NHDF-Ad	bronchial
29	chr1:161702800-161704000	Enhancers	HSMM	muscle
30	chr1:161702800-161704000	Enhancers	HUVEC	blood vessel
31	chr1:161702800-161704000	Enhancers	NHLF	lung
32	chr1:161702800-161704200	Enhancers	Osteobl	bone
33	chr1:161703000-161704000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:161703000-161704000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:161703000-161704000	Enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links