Variant report

Variant	rs1538971
Chromosome Location	chr1:161676394-161676395
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	GATA3	chr1:161675907-161676881	SK-N-SH	brain:	n/a	chr1:161676272-161676285 chr1:161676270-161676281 chr1:161676535-161676542 chr1:161676334-161676341
2	FOSL2	chr1:161676143-161676871	SK-N-SH	brain:	n/a	n/a
3	RUNX3	chr1:161675271-161677304	GM12878	blood:	n/a	n/a
4	MTA3	chr1:161675888-161677287	GM12878	blood:	n/a	n/a
5	PML	chr1:161676308-161677223	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:161675835-161676863	U87	brain:	n/a	n/a
7	RUNX3	chr1:161675286-161677289	GM12878	blood:	n/a	n/a
8	ELF1	chr1:161676366-161677240	GM12878	blood:	n/a	chr1:161676975-161676986 chr1:161676369-161676380
9	JUN	chr1:161676267-161676956	K562	blood:	n/a	n/a
10	REST	chr1:161676258-161676497	K562	blood:	n/a	n/a
11	EP300	chr1:161676290-161677140	K562	blood:	n/a	chr1:161676971-161676985 chr1:161676975-161676984
12	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
13	POLR2A	chr1:161676318-161677246	GM15510	blood:	n/a	n/a
14	EP300	chr1:161676134-161676788	SK-N-SH	brain:	n/a	n/a
15	ATF3	chr1:161676229-161676963	K562	blood:	n/a	n/a
16	BHLHE40	chr1:161676187-161677219	K562	blood:	n/a	n/a
17	POLR2A	chr1:161676217-161678036	GM12892	blood:	n/a	n/a
18	MEF2A	chr1:161676072-161676934	SK-N-SH	brain:	n/a	chr1:161676446-161676461
19	NFYB	chr1:161676394-161677117	GM12878	blood:	n/a	n/a
20	MAZ	chr1:161676298-161677051	K562	blood:	n/a	chr1:161676704-161676713
21	TBL1XR1	chr1:161676293-161677116	K562	blood:	n/a	n/a
22	RCOR1	chr1:161676279-161677221	K562	blood:	n/a	n/a
23	SETDB1	chr1:161676092-161676938	U2OS	brain:	n/a	n/a
24	ATF2	chr1:161675907-161677472	GM12878	blood:	n/a	n/a
25	JUN	chr1:161676271-161676665	K562	blood:	n/a	n/a
26	POLR2A	chr1:161676359-161677266	GM12892	blood:	n/a	n/a
27	POLR2A	chr1:161675236-161678018	Raji	blood:	n/a	n/a
28	POLR2A	chr1:161676391-161677667	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:161675911-161676739	U87	brain:	n/a	n/a
30	ATF3	chr1:161676291-161676537	K562	blood:	n/a	n/a
31	NR2F2	chr1:161676311-161677260	K562	blood:	n/a	n/a
32	BCL11A	chr1:161676167-161677205	GM12878	blood:	n/a	chr1:161676927-161676936
33	KAP1	chr1:161676020-161676966	U2OS	brain:	n/a	n/a
34	MEF2A	chr1:161676006-161677360	GM12878	blood:	n/a	chr1:161676446-161676461
35	IRF4	chr1:161676210-161677313	GM12878	blood:	n/a	n/a
36	JUN	chr1:161676257-161676988	K562	blood:	n/a	n/a
37	RELA	chr1:161676014-161677202	GM10847	blood:	n/a	n/a
38	STAT5A	chr1:161676130-161677259	GM12878	blood:	n/a	chr1:161676414-161676421
39	JUND	chr1:161676208-161677129	K562	blood:	n/a	n/a
40	RELA	chr1:161676151-161677242	GM19099	blood:	n/a	n/a
41	MEF2A	chr1:161676245-161676674	K562	blood:	n/a	chr1:161676446-161676461
42	POU2F2	chr1:161676330-161676587	GM12878	blood:	n/a	chr1:161676486-161676496 chr1:161676486-161676498 chr1:161676477-161676495 chr1:161676475-161676497 chr1:161676482-161676489 chr1:161676481-161676490 chr1:161676481-161676492 chr1:161676482-161676500 chr1:161676488-161676495 chr1:161676485-161676496 chr1:161676485-161676498 chr1:161676481-161676491 chr1:161676487-161676496 chr1:161676484-161676499 chr1:161676478-161676493
43	MYC	chr1:161676090-161676968	MCF10A-Er-Src	breast:	n/a	chr1:161676704-161676713
44	E2F4	chr1:161676392-161676645	MCF10A-Er-Src	breast:	n/a	chr1:161676628-161676637
45	IKZF1	chr1:161676040-161677114	GM12878	blood:	n/a	n/a
46	STAT3	chr1:161676324-161676844	MCF10A-Er-Src	breast:	n/a	chr1:161676414-161676421
47	MEF2A	chr1:161676165-161676735	K562	blood:	n/a	chr1:161676446-161676461
48	POLR2A	chr1:161676232-161677525	GM18505	blood:	n/a	n/a
49	POU2F2	chr1:161676239-161677247	GM12891	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
50	POU2F2	chr1:161676245-161676610	GM12878	blood:	n/a	chr1:161676486-161676496 chr1:161676486-161676498 chr1:161676477-161676495 chr1:161676475-161676497 chr1:161676482-161676489 chr1:161676481-161676490 chr1:161676481-161676492 chr1:161676482-161676500 chr1:161676488-161676495 chr1:161676485-161676496 chr1:161676485-161676498 chr1:161676481-161676491 chr1:161676487-161676496 chr1:161676484-161676499 chr1:161676478-161676493

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:161667779..161671071-chr1:161673847..161676940,3	K562	blood:
2	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: 23 )
Associated
traits (count: 9 )

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];0.92[ASN][1000 genomes]
rs12408296	0.86[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs1340977	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1340978	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]
rs1340979	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]
rs1340980	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[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];0.82[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];0.83[ASN][1000 genomes]
rs1954173	0.94[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4657093	0.87[CHB][hapmap];0.80[CHD][hapmap]
rs57678166	0.81[ASN][1000 genomes]
rs74127102	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	esv2753408	chr1:161514302-161676557	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv429825	chr1:161514302-161676557	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	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
11	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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1538971	NDUFS2	cis	parietal	SCAN
rs1538971	FCGR2B	cis	lymphoblastoid	seeQTL
rs1538971	FCRLA	cis	lymphoblastoid	seeQTL
rs1538971	FCRLA	cis	Lymphoblastoid	GTEx
rs1538971	CD1E	cis	cerebellum	SCAN
rs1538971	FCGR2C	cis	lymphoblastoid	seeQTL
rs1538971	NTRK1	cis	parietal	SCAN
rs1538971	FCRLA	Cis_1M	lymphoblastoid	RTeQTL
rs1538971	FCRLA	cis	multi-tissue	Pritchard

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161672800-161676400	Weak transcription	HepG2	liver
2	chr1:161674400-161676400	Enhancers	Primary B cells from peripheral blood	blood
3	chr1:161674800-161676600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:161675400-161676600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:161675400-161676800	Flanking Active TSS	GM12878-XiMat	blood
6	chr1:161675400-161677000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:161675400-161677600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:161675400-161677600	Enhancers	HMEC	breast
9	chr1:161675400-161677600	Enhancers	HSMM	muscle
10	chr1:161675400-161677600	Enhancers	NHLF	lung
11	chr1:161675400-161678200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:161675400-161678400	Enhancers	NHDF-Ad	bronchial
13	chr1:161675800-161677000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:161675800-161677200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:161675800-161677200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:161675800-161677400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:161675800-161680600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr1:161676000-161676400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:161676000-161676400	Flanking Active TSS	Osteobl	bone
20	chr1:161676000-161676600	Enhancers	Brain Substantia Nigra	brain
21	chr1:161676000-161676600	Enhancers	HSMMtube	muscle
22	chr1:161676000-161676800	Enhancers	Right Atrium	heart
23	chr1:161676000-161676800	Enhancers	Hela-S3	cervix
24	chr1:161676000-161677200	Enhancers	Brain Angular Gyrus	brain
25	chr1:161676000-161677200	Enhancers	Brain Anterior Caudate	brain
26	chr1:161676000-161677200	Enhancers	Brain Hippocampus Middle	brain
27	chr1:161676000-161677200	Enhancers	Fetal Muscle Leg	muscle
28	chr1:161676000-161677200	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr1:161676000-161677200	Enhancers	NHEK	skin
30	chr1:161676000-161677400	Enhancers	Brain Cingulate Gyrus	brain
31	chr1:161676000-161677600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:161676000-161677600	Enhancers	Left Ventricle	heart
33	chr1:161676000-161677600	Enhancers	K562	blood
34	chr1:161676000-161677800	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr1:161676000-161679800	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr1:161676200-161676400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:161676200-161676400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr1:161676200-161676400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:161676200-161676400	Flanking Active TSS	NH-A	brain
40	chr1:161676200-161676800	Enhancers	Adipose Nuclei	Adipose
41	chr1:161676200-161677000	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr1:161676200-161677000	Bivalent Enhancer	Fetal Heart	heart
43	chr1:161676200-161677200	Enhancers	Psoas Muscle	Psoas
44	chr1:161676200-161692000	Weak transcription	Spleen	Spleen

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