Variant report

Variant	rs61942830
Chromosome Location	chr12:48840305-48840306
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	FOS	chr12:48840194-48840611	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr12:48840200-48840599	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr12:48840031-48840422	Hela-S3	cervix:	n/a	chr12:48840193-48840202 chr12:48840193-48840204
4	STAT3	chr12:48840223-48840605	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr12:48840037-48840556	MCF10A-Er-Src	breast:	n/a	chr12:48840130-48840141 chr12:48840193-48840201
6	MEF2A	chr12:48840237-48840638	GM12878	blood:	n/a	chr12:48840453-48840464 chr12:48840450-48840471 chr12:48840452-48840467 chr12:48840454-48840465 chr12:48840451-48840467 chr12:48840455-48840464 chr12:48840451-48840466 chr12:48840452-48840466 chr12:48840450-48840471
7	FOS	chr12:48840276-48840582	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr12:48840274-48840597	MCF10A-Er-Src	breast:	n/a	n/a
9	BCL11A	chr12:48840253-48840465	H1-hESC	embryonic stem cell:	n/a	n/a
10	EBF1	chr12:48840215-48840598	GM12878	blood:	n/a	n/a
11	NFIC	chr12:48839824-48840673	GM12878	blood:	n/a	n/a
12	FOS	chr12:48840256-48840563	MCF10A-Er-Src	breast:	n/a	n/a
13	STAT3	chr12:48840188-48840582	MCF10A-Er-Src	breast:	n/a	chr12:48840193-48840201
14	EBF1	chr12:48840189-48840491	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
OR8T1P	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11168613	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12578360	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12580859	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12581223	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12582586	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12582594	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17234937	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28889727	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4397895	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4426170	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4485148	0.87[AFR][1000 genomes]
rs4547144	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55647233	0.90[ASN][1000 genomes]
rs55667337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55971664	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55983865	0.95[EUR][1000 genomes]
rs56034252	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56191575	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59325389	0.87[AFR][1000 genomes]
rs59337124	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61940763	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61940764	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61940766	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61940767	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61940768	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61940776	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61940777	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61940779	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61940780	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61940822	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61942782	0.87[AFR][1000 genomes]
rs61942783	0.87[AFR][1000 genomes]
rs61942784	0.87[AFR][1000 genomes]
rs61942785	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs61942786	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61942787	0.86[AMR][1000 genomes]
rs61942812	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61942813	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61942816	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61942817	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61942828	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942829	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv977157	chr12:48839854-48852791	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48833800-48840400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr12:48834200-48840400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:48834200-48840400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:48839200-48840400	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr12:48839200-48840400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr12:48839400-48840400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:48839400-48840400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr12:48839400-48840400	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr12:48839600-48840400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:48839600-48840400	Enhancers	Hela-S3	cervix
11	chr12:48839600-48841000	Enhancers	Fetal Heart	heart
12	chr12:48839600-48841200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:48839800-48840400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:48839800-48840400	Enhancers	Primary T cells fromperipheralblood	blood
15	chr12:48839800-48840400	Enhancers	Psoas Muscle	Psoas
16	chr12:48839800-48840400	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr12:48839800-48840400	Enhancers	GM12878-XiMat	blood
18	chr12:48839800-48840400	Bivalent Enhancer	HUVEC	blood vessel
19	chr12:48839800-48840600	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr12:48839800-48840600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:48840000-48840400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr12:48840200-48840400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:48840200-48841200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:48840200-48841600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr12:48840200-48841600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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