Variant report

Variant	rs1340979
Chromosome Location	chr1:161677350-161677351
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	SPI1	chr1:161677318-161677589	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:161676217-161678036	GM12892	blood:	n/a	n/a
3	ATF2	chr1:161675907-161677472	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:161675236-161678018	Raji	blood:	n/a	n/a
5	POLR2A	chr1:161676391-161677667	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:161676470-161677700	GM12892	blood:	n/a	n/a
7	SPI1	chr1:161677274-161677603	GM12891	blood:	n/a	n/a
8	MEF2A	chr1:161676006-161677360	GM12878	blood:	n/a	chr1:161676446-161676461
9	CUX1	chr1:161677350-161677545	GM12878	blood:	n/a	n/a
10	SPI1	chr1:161677245-161677618	GM12891	blood:	n/a	n/a
11	POLR2A	chr1:161676232-161677525	GM18505	blood:	n/a	n/a
12	STAT5A	chr1:161675882-161677406	GM12878	blood:	n/a	chr1:161676414-161676421
13	POLR2A	chr1:161676218-161678545	GM12891	blood:	n/a	n/a
14	CEBPB	chr1:161676088-161677659	GM12878	blood:	n/a	chr1:161676701-161676712
15	BCLAF1	chr1:161676190-161677368	GM12878	blood:	n/a	chr1:161676927-161676936
16	JUN	chr1:161675718-161677686	K562	blood:	n/a	n/a
17	PML	chr1:161675867-161678178	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:161676349-161677588	GM19099	blood:	n/a	n/a
19	NFIC	chr1:161675191-161677857	GM12878	blood:	n/a	chr1:161676310-161676327 chr1:161676310-161676326
20	POLR2A	chr1:161676459-161678261	GM12892	blood:	n/a	n/a
21	BHLHE40	chr1:161676132-161677400	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:161676285-161678577	GM12878	blood:	n/a	n/a
23	MTA3	chr1:161675256-161678479	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:161676369-161677581	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:161676249-161677718	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:161677121..161679577-chr1:161693042..161696902,4	MCF-7	breast:
2	chr1:161667456..161669424-chr1:161676316..161679255,2	MCF-7	breast:

Variant related genes	Relation type
FCRLA	TF binding region
ENSG00000162746	Chromatin interaction
ENSG00000199595	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10917750	0.93[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs12408296	0.86[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs1340977	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1340978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1340980	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1417582	0.84[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1538971	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1891020	0.84[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1954173	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657093	0.87[CHB][hapmap];0.85[CHD][hapmap]
rs57678166	0.82[ASN][1000 genomes]
rs74127102	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756866	chr1:161344255-161681552	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	esv2758972	chr1:161344255-161681552	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	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
4	esv2755678	chr1:161463498-161678377	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	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
6	esv1822760	chr1:161480943-161687379	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	esv1817508	chr1:161483404-161678548	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	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
9	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1340979	FCGR2C	cis	lymphoblastoid	seeQTL
rs1340979	FCRLA	cis	multi-tissue	Pritchard
rs1340979	FCGR2B	cis	multi-tissue	Pritchard
rs1340979	CD1E	cis	cerebellum	SCAN
rs1340979	FCGR2B	cis	lymphoblastoid	seeQTL
rs1340979	FCRLA	cis	lymphoblastoid	seeQTL
rs1340979	FCRLM2	cis	multi-tissue	Pritchard
rs1340979	FCRLA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161675400-161677600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:161675400-161677600	Enhancers	HMEC	breast
3	chr1:161675400-161677600	Enhancers	HSMM	muscle
4	chr1:161675400-161677600	Enhancers	NHLF	lung
5	chr1:161675400-161678200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:161675400-161678400	Enhancers	NHDF-Ad	bronchial
7	chr1:161675800-161677400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:161675800-161680600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr1:161676000-161677400	Enhancers	Brain Cingulate Gyrus	brain
10	chr1:161676000-161677600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:161676000-161677600	Enhancers	Left Ventricle	heart
12	chr1:161676000-161677600	Enhancers	K562	blood
13	chr1:161676000-161677800	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr1:161676000-161679800	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr1:161676200-161692000	Weak transcription	Spleen	Spleen
16	chr1:161676400-161677400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
17	chr1:161676400-161677400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
18	chr1:161676400-161677600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:161676600-161678600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:161676800-161679600	Active TSS	GM12878-XiMat	blood
21	chr1:161676800-161679800	Weak transcription	Right Atrium	heart
22	chr1:161677000-161677600	Active TSS	Primary B cells from peripheral blood	blood
23	chr1:161677000-161677600	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr1:161677000-161677800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:161677000-161678000	Enhancers	Osteobl	bone
26	chr1:161677000-161679200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:161677200-161677800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:161677200-161677800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:161677200-161678000	Enhancers	HSMMtube	muscle
30	chr1:161677200-161679400	Weak transcription	Brain Hippocampus Middle	brain

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