Variant report

Variant	rs3743486
Chromosome Location	chr15:75113958-75113959
allele	C/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	POLR2A	chr15:75113546-75114186	Raji	blood:	n/a	n/a
2	MAX	chr15:75113789-75114040	NB4	blood:	n/a	n/a
3	EBF1	chr15:75113846-75114067	GM12878	blood:	n/a	chr15:75113938-75113947
4	POU2F2	chr15:75113516-75114104	GM12891	blood:	n/a	chr15:75113842-75113852 chr15:75113839-75113852 chr15:75113866-75113873 chr15:75113865-75113874 chr15:75113840-75113853 chr15:75113841-75113851 chr15:75113843-75113850 chr15:75113842-75113853 chr15:75113865-75113875 chr15:75113861-75113879 chr15:75113838-75113856 chr15:75113840-75113854 chr15:75113864-75113874 chr15:75113840-75113852 chr15:75113842-75113853 chr15:75113842-75113851 chr15:75113839-75113854 chr15:75113864-75113874 chr15:75113866-75113874 chr15:75113841-75113851
5	ESR1	chr15:75113792-75114221	T-47D	breast:	n/a	n/a
6	POU2F2	chr15:75113714-75113963	GM12878	blood:	n/a	chr15:75113842-75113852 chr15:75113839-75113852 chr15:75113866-75113873 chr15:75113865-75113874 chr15:75113840-75113853 chr15:75113841-75113851 chr15:75113843-75113850 chr15:75113842-75113853 chr15:75113865-75113875 chr15:75113861-75113879 chr15:75113838-75113856 chr15:75113840-75113854 chr15:75113864-75113874 chr15:75113840-75113852 chr15:75113842-75113853 chr15:75113842-75113851 chr15:75113839-75113854 chr15:75113864-75113874 chr15:75113866-75113874 chr15:75113841-75113851
7	FOS	chr15:75113799-75114067	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr15:75113858-75113994	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr15:75113806-75114060	MCF10A-Er-Src	breast:	n/a	n/a
10	MYC	chr15:75113845-75114072	MCF10A-Er-Src	breast:	n/a	n/a
11	POU2F2	chr15:75113586-75114086	GM12878	blood:	n/a	chr15:75113842-75113852 chr15:75113839-75113852 chr15:75113866-75113873 chr15:75113865-75113874 chr15:75113840-75113853 chr15:75113841-75113851 chr15:75113843-75113850 chr15:75113842-75113853 chr15:75113865-75113875 chr15:75113861-75113879 chr15:75113838-75113856 chr15:75113840-75113854 chr15:75113864-75113874 chr15:75113840-75113852 chr15:75113842-75113853 chr15:75113842-75113851 chr15:75113839-75113854 chr15:75113864-75113874 chr15:75113866-75113874 chr15:75113841-75113851
12	FOS	chr15:75113835-75114073	MCF10A-Er-Src	breast:	n/a	n/a
13	GATA3	chr15:75113811-75114097	MCF-7	breast:	n/a	n/a
14	CEBPB	chr15:75113718-75114065	Hela-S3	cervix:	n/a	n/a
15	GATA3	chr15:75113751-75114092	T-47D	breast:	n/a	n/a
16	POU2F2	chr15:75113586-75114101	GM12891	blood:	n/a	chr15:75113842-75113852 chr15:75113839-75113852 chr15:75113866-75113873 chr15:75113865-75113874 chr15:75113840-75113853 chr15:75113841-75113851 chr15:75113843-75113850 chr15:75113842-75113853 chr15:75113865-75113875 chr15:75113861-75113879 chr15:75113838-75113856 chr15:75113840-75113854 chr15:75113864-75113874 chr15:75113840-75113852 chr15:75113842-75113853 chr15:75113842-75113851 chr15:75113839-75113854 chr15:75113864-75113874 chr15:75113866-75113874 chr15:75113841-75113851
17	ESR1	chr15:75113859-75114116	T-47D	breast:	n/a	n/a
18	MEF2A	chr15:75113637-75114073	GM12878	blood:	n/a	chr15:75113820-75113834

No.	Distal block	Cell Line	Cell type
1	chr15:75074174..75075858-chr15:75112738..75114767,2	MCF-7	breast:
2	chr15:75072350..75078841-chr15:75107920..75114107,12	MCF-7	breast:
3	chr15:75074461..75076806-chr15:75112062..75114585,2	K562	blood:
4	chr15:75113859..75115829-chr15:75135120..75137203,2	MCF-7	breast:
5	chr15:75111167..75114133-chr15:75116068..75118230,2	K562	blood:
6	chr15:75109449..75112132-chr15:75112266..75114045,2	MCF-7	breast:
7	chr15:75108356..75114001-chr15:75126388..75130558,9	MCF-7	breast:
8	chr15:75112517..75114870-chr15:75115640..75117170,2	MCF-7	breast:
9	chr15:75113543..75115731-chr15:75122217..75124290,2	K562	blood:

Variant related genes	Relation type
LMAN1L	TF binding region
CPLX3	TF binding region
ENSG00000140474	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000140506	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12438333	1.00[CEU][hapmap]
rs12439525	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12439944	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12441444	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12443172	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12593251	0.92[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs12594158	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1531162	1.00[CEU][hapmap];0.92[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1531163	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16972714	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2229730	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305667	0.82[CEU][hapmap];0.84[GIH][hapmap]
rs28397782	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28431073	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28577988	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28583379	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2899827	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3743484	0.81[JPT][hapmap]
rs3743487	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs3803568	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886409	0.84[ASW][hapmap];1.00[CEU][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4886620	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886627	0.84[AMR][1000 genomes]
rs7163332	0.86[TSI][hapmap]
rs7165811	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs8039046	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9796628	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[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	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv520527	chr15:75108636-75122856	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75107200-75114400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:75109800-75116800	Weak transcription	Brain Anterior Caudate	brain
3	chr15:75110800-75115000	Enhancers	Primary B cells from peripheral blood	blood
4	chr15:75111400-75128000	Weak transcription	Gastric	stomach
5	chr15:75112400-75114400	Enhancers	Primary B cells from cord blood	blood
6	chr15:75112400-75114800	Enhancers	Fetal Brain Male	brain
7	chr15:75112600-75114200	Bivalent Enhancer	Placenta	Placenta
8	chr15:75112600-75114400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:75112800-75114400	Enhancers	GM12878-XiMat	blood
10	chr15:75113000-75114000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr15:75113000-75114200	Enhancers	Esophagus	oesophagus
12	chr15:75113000-75114400	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr15:75113000-75114400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:75113000-75115000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:75113200-75114000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:75113200-75114000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:75113200-75114000	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr15:75113200-75114000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:75113200-75114200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr15:75113200-75114200	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr15:75113200-75114400	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr15:75113200-75114400	Enhancers	H1 Cell Line	embryonic stem cell
23	chr15:75113200-75114400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:75113200-75114400	Enhancers	Hela-S3	cervix
25	chr15:75113400-75114200	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr15:75113400-75114600	Enhancers	Spleen	Spleen
27	chr15:75113600-75114000	Flanking Active TSS	Brain Germinal Matrix	brain
28	chr15:75113600-75114400	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr15:75113600-75118600	Weak transcription	Right Atrium	heart
30	chr15:75113800-75114000	Enhancers	H9 Cell Line	embryonic stem cell
31	chr15:75113800-75114000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:75113800-75114000	Flanking Active TSS	Fetal Brain Female	brain
33	chr15:75113800-75114000	Enhancers	A549	lung
34	chr15:75113800-75114200	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr15:75113800-75114200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:75113800-75114400	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr15:75113800-75115200	Weak transcription	Duodenum Mucosa	Duodenum

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