Variant report

Variant	rs1340978
Chromosome Location	chr1:161676970-161676971
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	HDAC2	chr1:161676593-161677228	K562	blood:	n/a	chr1:161676972-161676986
2	TAF1	chr1:161676823-161677153	GM12878	blood:	n/a	n/a
3	RUNX3	chr1:161675271-161677304	GM12878	blood:	n/a	n/a
4	TAL1	chr1:161676704-161677085	K562	blood:	n/a	n/a
5	MTA3	chr1:161675888-161677287	GM12878	blood:	n/a	n/a
6	TAF1	chr1:161676909-161677187	GM12892	blood:	n/a	n/a
7	POLR2A	chr1:161676532-161677323	GM12878	blood:	n/a	n/a
8	PML	chr1:161676308-161677223	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:161676644-161677206	K562	blood:	n/a	n/a
10	HEY1	chr1:161676842-161677073	K562	blood:	n/a	n/a
11	RUNX3	chr1:161675286-161677289	GM12878	blood:	n/a	n/a
12	ELF1	chr1:161676366-161677240	GM12878	blood:	n/a	chr1:161676975-161676986 chr1:161676369-161676380
13	NR2F2	chr1:161676567-161677141	K562	blood:	n/a	n/a
14	EP300	chr1:161676290-161677140	K562	blood:	n/a	chr1:161676971-161676985 chr1:161676975-161676984
15	POU2F2	chr1:161676887-161677208	GM12878	blood:	n/a	chr1:161677144-161677158 chr1:161677145-161677153 chr1:161677139-161677160 chr1:161677144-161677155
16	POU2F2	chr1:161676219-161677315	GM12878	blood:	n/a	chr1:161676486-161676496 chr1:161676486-161676498 chr1:161676477-161676495 chr1:161676475-161676497 chr1:161676482-161676489 chr1:161676481-161676490 chr1:161676778-161676791 chr1:161677144-161677158 chr1:161676481-161676492 chr1:161676482-161676500 chr1:161676488-161676495 chr1:161676485-161676496 chr1:161676485-161676498 chr1:161676481-161676491 chr1:161677145-161677153 chr1:161676487-161676496 chr1:161676484-161676499 chr1:161677139-161677160 chr1:161676478-161676493 chr1:161677144-161677155
17	POLR2A	chr1:161676318-161677246	GM15510	blood:	n/a	n/a
18	POLR2A	chr1:161676623-161677189	K562	blood:	n/a	n/a
19	POLR2A	chr1:161676889-161677017	MCF10A-Er-Src	breast:	n/a	n/a
20	BHLHE40	chr1:161676187-161677219	K562	blood:	n/a	n/a
21	POLR2A	chr1:161676217-161678036	GM12892	blood:	n/a	n/a
22	CEBPD	chr1:161676474-161677252	K562	blood:	n/a	n/a
23	NFYB	chr1:161676394-161677117	GM12878	blood:	n/a	n/a
24	MAZ	chr1:161676298-161677051	K562	blood:	n/a	chr1:161676704-161676713
25	TBL1XR1	chr1:161676293-161677116	K562	blood:	n/a	n/a
26	RCOR1	chr1:161676279-161677221	K562	blood:	n/a	n/a
27	RCOR1	chr1:161676401-161677210	K562	blood:	n/a	n/a
28	MAFK	chr1:161676428-161677033	K562	blood:	n/a	n/a
29	ATF2	chr1:161675907-161677472	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:161676359-161677266	GM12892	blood:	n/a	n/a
31	POLR2A	chr1:161675236-161678018	Raji	blood:	n/a	n/a
32	POLR2A	chr1:161676391-161677667	GM12878	blood:	n/a	n/a
33	CBX3	chr1:161676521-161677151	K562	blood:	n/a	n/a
34	POLR2A	chr1:161676537-161677055	K562	blood:	n/a	n/a
35	IRF4	chr1:161676470-161677107	GM12878	blood:	n/a	n/a
36	POLR2A	chr1:161676470-161677700	GM12892	blood:	n/a	n/a
37	POU2F2	chr1:161676679-161677188	GM12878	blood:	n/a	chr1:161676778-161676791 chr1:161677144-161677158 chr1:161677145-161677153 chr1:161677139-161677160 chr1:161677144-161677155
38	NR2F2	chr1:161676311-161677260	K562	blood:	n/a	n/a
39	YY1	chr1:161676541-161677025	K562	blood:	n/a	n/a
40	BCL11A	chr1:161676167-161677205	GM12878	blood:	n/a	chr1:161676927-161676936
41	TAF7	chr1:161676640-161676984	K562	blood:	n/a	n/a
42	MEF2A	chr1:161676006-161677360	GM12878	blood:	n/a	chr1:161676446-161676461
43	IRF4	chr1:161676210-161677313	GM12878	blood:	n/a	n/a
44	TCF3	chr1:161676653-161677155	GM12878	blood:	n/a	n/a
45	JUN	chr1:161676257-161676988	K562	blood:	n/a	n/a
46	YY1	chr1:161676537-161677222	GM12878	blood:	n/a	n/a
47	TAF1	chr1:161676806-161677186	GM12891	blood:	n/a	n/a
48	RELA	chr1:161676014-161677202	GM10847	blood:	n/a	n/a
49	STAT5A	chr1:161676130-161677259	GM12878	blood:	n/a	chr1:161676414-161676421
50	JUND	chr1:161676208-161677129	K562	blood:	n/a	n/a

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

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

Extended variants
information (count: 21 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs10917750	0.93[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs12408296	0.86[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs1340977	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1340979	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	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1417582	0.84[CEU][hapmap];0.93[CHB][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1538971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1891020	0.84[CEU][hapmap];0.93[CHB][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1954173	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4657093	0.87[CHB][hapmap];0.80[CHD][hapmap]
rs57678166	0.83[ASN][1000 genomes]
rs74127102	0.84[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1340978	FCRLA	cis	multi-tissue	Pritchard
rs1340978	FCGR2C	cis	lymphoblastoid	seeQTL
rs1340978	FCGR2B	cis	lymphoblastoid	seeQTL
rs1340978	FCRLM2	cis	multi-tissue	Pritchard
rs1340978	ENSG00000132185	cis	multi-tissue	Pritchard
rs1340978	CD1E	cis	cerebellum	SCAN
rs1340978	NTRK1	cis	parietal	SCAN
rs1340978	FCGR2B	cis	multi-tissue	Pritchard
rs1340978	FCRLA	cis	lymphoblastoid	seeQTL
rs1340978	FCRLA	cis	Lymphoblastoid	GTEx
rs1340978	NDUFS2	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161675400-161677000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:161675400-161677600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:161675400-161677600	Enhancers	HMEC	breast
4	chr1:161675400-161677600	Enhancers	HSMM	muscle
5	chr1:161675400-161677600	Enhancers	NHLF	lung
6	chr1:161675400-161678200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:161675400-161678400	Enhancers	NHDF-Ad	bronchial
8	chr1:161675800-161677000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:161675800-161677200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:161675800-161677200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:161675800-161677400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:161675800-161680600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr1:161676000-161677200	Enhancers	Brain Angular Gyrus	brain
14	chr1:161676000-161677200	Enhancers	Brain Anterior Caudate	brain
15	chr1:161676000-161677200	Enhancers	Brain Hippocampus Middle	brain
16	chr1:161676000-161677200	Enhancers	Fetal Muscle Leg	muscle
17	chr1:161676000-161677200	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr1:161676000-161677200	Enhancers	NHEK	skin
19	chr1:161676000-161677400	Enhancers	Brain Cingulate Gyrus	brain
20	chr1:161676000-161677600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:161676000-161677600	Enhancers	Left Ventricle	heart
22	chr1:161676000-161677600	Enhancers	K562	blood
23	chr1:161676000-161677800	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr1:161676000-161679800	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr1:161676200-161677000	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr1:161676200-161677000	Bivalent Enhancer	Fetal Heart	heart
27	chr1:161676200-161677200	Enhancers	Psoas Muscle	Psoas
28	chr1:161676200-161692000	Weak transcription	Spleen	Spleen
29	chr1:161676400-161677000	Flanking Active TSS	Primary B cells from peripheral blood	blood
30	chr1:161676400-161677400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
31	chr1:161676400-161677400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
32	chr1:161676400-161677600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:161676600-161677000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr1:161676600-161677000	Flanking Active TSS	Osteobl	bone
35	chr1:161676600-161677200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:161676600-161678600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:161676800-161677000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:161676800-161677000	Enhancers	HSMMtube	muscle
39	chr1:161676800-161677200	Enhancers	NH-A	brain
40	chr1:161676800-161679600	Active TSS	GM12878-XiMat	blood
41	chr1:161676800-161679800	Weak transcription	Right Atrium	heart

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