Variant report

Variant	rs13377939
Chromosome Location	chr12:9878089-9878090
allele	G/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	CEBPB	chr12:9877876-9878132	H1-hESC	embryonic stem cell:	n/a	n/a
2	FOS	chr12:9877818-9878223	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr12:9877858-9878158	K562	blood:	n/a	n/a
4	STAT3	chr12:9877829-9878374	MCF10A-Er-Src	breast:	n/a	chr12:9878075-9878086
5	FOS	chr12:9877766-9878399	MCF10A-Er-Src	breast:	n/a	n/a
6	CEBPB	chr12:9877847-9878164	HepG2	liver:	n/a	n/a
7	CEBPB	chr12:9877855-9878176	Hela-S3	cervix:	n/a	n/a
8	STAT3	chr12:9877997-9878724	MCF10A-Er-Src	breast:	n/a	chr12:9878075-9878086
9	CEBPB	chr12:9877819-9878188	A549	lung:	n/a	n/a
10	CEBPB	chr12:9877828-9878178	IMR90	lung:	n/a	n/a
11	FOS	chr12:9877850-9878427	MCF10A-Er-Src	breast:	n/a	n/a
12	MYC	chr12:9877961-9878331	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:9876569..9878295-chr12:9885822..9888452,2	K562	blood:
2	chr12:9876110..9878240-chr12:9880296..9883371,3	K562	blood:
3	chr12:9792708..9795930-chr12:9875976..9879286,3	K562	blood:

Variant related genes	Relation type
CLECL1	TF binding region
ENSG00000233719	Chromatin interaction
ENSG00000184293	Chromatin interaction
ENSG00000272917	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10161013	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10492164	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10743828	0.93[EUR][1000 genomes]
rs10772093	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10772099	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10844656	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs11052306	0.80[EUR][1000 genomes]
rs1134543	0.86[EUR][1000 genomes]
rs11835594	0.85[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304982	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12820281	0.97[EUR][1000 genomes]
rs12824727	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13377908	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16914640	0.85[CEU][hapmap]
rs16923367	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs16927874	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080210	0.85[EUR][1000 genomes]
rs2268145	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2401387	0.86[EUR][1000 genomes]
rs2401388	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs3136576	0.80[EUR][1000 genomes]
rs34584384	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34633868	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35990903	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3922289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4611290	0.86[EUR][1000 genomes]
rs4763296	0.82[EUR][1000 genomes]
rs4763864	0.84[EUR][1000 genomes]
rs55715780	0.86[EUR][1000 genomes]
rs56980650	0.86[EUR][1000 genomes]
rs59016059	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59210706	0.86[EUR][1000 genomes]
rs6488110	0.81[EUR][1000 genomes]
rs6488120	0.84[EUR][1000 genomes]
rs6488121	0.84[EUR][1000 genomes]
rs6488123	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6488176	0.91[EUR][1000 genomes]
rs71447599	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71447600	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301386	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74062704	0.86[EUR][1000 genomes]
rs74062708	0.89[EUR][1000 genomes]
rs74065337	0.86[EUR][1000 genomes]
rs74065339	0.86[EUR][1000 genomes]
rs74065340	0.86[EUR][1000 genomes]
rs7962964	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964917	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967436	0.84[EUR][1000 genomes]
rs7969022	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs7976474	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv983235	chr12:9852218-9893776	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv2757490	chr12:9855958-9888553	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13377939	RP11-75L1.2	cis	lung	GTEx
rs13377939	RP11-75L1.2	cis	Skin Sun Exposed Lower leg	GTEx
rs13377939	RP11-75L1.2	cis	Whole Blood	GTEx
rs13377939	RP11-75L1.2	cis	Adipose Subcutaneous	GTEx
rs13377939	RP11-75L1.2	cis	Nerve Tibial	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9861600-9882400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:9864600-9883800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr12:9868600-9879200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:9874400-9881400	Enhancers	Primary B cells from cord blood	blood
5	chr12:9875000-9881200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr12:9875600-9880000	Weak transcription	HUVEC	blood vessel
7	chr12:9876800-9878200	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr12:9876800-9878200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr12:9877400-9878600	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr12:9877800-9878600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:9877800-9878600	Enhancers	NHEK	skin
12	chr12:9878000-9878200	Active TSS	GM12878-XiMat	blood
13	chr12:9878000-9878400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:9878000-9878600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:9878000-9878600	Enhancers	HMEC	breast

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