Variant report

Variant	rs7738052
Chromosome Location	chr6:113755456-113755457
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	GATA3	chr6:113753742-113755812	MCF-7	breast:	n/a	chr6:113753875-113753885 chr6:113755373-113755389 chr6:113755377-113755384 chr6:113755377-113755384 chr6:113755375-113755387 chr6:113755377-113755384
2	GATA3	chr6:113753824-113755522	A549	lung:	n/a	chr6:113753875-113753885 chr6:113755373-113755389 chr6:113755377-113755384 chr6:113755377-113755384 chr6:113755375-113755387 chr6:113755377-113755384
3	GATA3	chr6:113755309-113755509	SH-SY5Y	brain:	n/a	chr6:113755373-113755389 chr6:113755377-113755384 chr6:113755377-113755384 chr6:113755375-113755387 chr6:113755377-113755384
4	GATA3	chr6:113753876-113755661	MCF-7	breast:	n/a	chr6:113755373-113755389 chr6:113755377-113755384 chr6:113755377-113755384 chr6:113755375-113755387 chr6:113755377-113755384
5	EP300	chr6:113753817-113755479	T-47D	breast:	n/a	chr6:113755150-113755160 chr6:113753975-113753989 chr6:113753976-113753984 chr6:113753873-113753887
6	TCF12	chr6:113754049-113755658	MCF-7	breast:	n/a	n/a
7	SIN3AK20	chr6:113753876-113755591	MCF-7	breast:	n/a	n/a
8	FOXM1	chr6:113753798-113755513	MCF-7	breast:	n/a	n/a
9	JUND	chr6:113753939-113755483	T-47D	breast:	n/a	chr6:113754145-113754157
10	JUND	chr6:113754276-113755469	T-47D	breast:	n/a	n/a
11	GATA3	chr6:113753995-113755569	T-47D	breast:	n/a	chr6:113755373-113755389 chr6:113755377-113755384 chr6:113755377-113755384 chr6:113755375-113755387 chr6:113755377-113755384
12	GATA3	chr6:113754069-113755578	MCF-7	breast:	n/a	chr6:113755373-113755389 chr6:113755377-113755384 chr6:113755377-113755384 chr6:113755375-113755387 chr6:113755377-113755384
13	CEBPB	chr6:113753789-113755513	MCF-7	breast:	n/a	chr6:113754871-113754882 chr6:113754869-113754882

No.	Distal block	Cell Line	Cell type
1	chr6:113753088..113757268-chr6:113951584..113954499,3	MCF-7	breast:
2	chr6:113750617..113753339-chr6:113755230..113758094,2	MCF-7	breast:
3	chr6:113753712..113755714-chr6:114178275..114180113,2	MCF-7	breast:
4	chr6:113755353..113757884-chr6:113758152..113760628,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232316	TF binding region
ENSG00000155130	Chromatin interaction
ENSG00000230943	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1009404	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10872098	0.89[ASN][1000 genomes]
rs11153416	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883171	0.86[ASN][1000 genomes]
rs2049923	0.89[ASN][1000 genomes]
rs2142639	0.89[ASN][1000 genomes]
rs2348293	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348294	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348295	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348302	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2881870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4945495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4945496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568788	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6568790	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs6568793	0.89[ASN][1000 genomes]
rs6903091	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6903628	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908767	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6915133	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915622	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6926220	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs718459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718460	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7341217	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7739755	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768104	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909541	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909543	0.81[MEX][hapmap]
rs9285410	0.81[MEX][hapmap]
rs9285411	0.89[ASN][1000 genomes]
rs9320446	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320450	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320459	0.89[ASN][1000 genomes]
rs9374397	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374401	0.89[ASN][1000 genomes]
rs9387145	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400624	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9481369	0.89[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	nsv916294	chr6:113518489-113904305	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1034256	chr6:113703567-113793790	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1021815	chr6:113703567-113799956	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1018357	chr6:113748468-113781070	Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7738052	RFPL4B	cis	cerebellum	SCAN
rs7738052	ROS1	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:113753000-113755800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr6:113753400-113755800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:113753600-113755600	Enhancers	Primary B cells from cord blood	blood
4	chr6:113753600-113755600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:113753600-113755800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:113753600-113755800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:113753600-113755800	Enhancers	NHDF-Ad	bronchial
8	chr6:113753600-113755800	Enhancers	NHLF	lung
9	chr6:113753600-113756200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:113753600-113756600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:113753600-113756800	Enhancers	Osteobl	bone
12	chr6:113753800-113756000	Enhancers	Placenta	Placenta
13	chr6:113753800-113756200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:113753800-113756600	Enhancers	Fetal Lung	lung
15	chr6:113754000-113755800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr6:113754200-113755600	Enhancers	Adipose Nuclei	Adipose
17	chr6:113754200-113755600	Enhancers	HMEC	breast
18	chr6:113754200-113755800	Enhancers	Fetal Intestine Small	intestine
19	chr6:113754200-113755800	Enhancers	Ovary	ovary
20	chr6:113754200-113756000	Enhancers	Colon Smooth Muscle	Colon
21	chr6:113754200-113756800	Enhancers	Fetal Stomach	stomach
22	chr6:113754400-113755600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr6:113754400-113755600	Enhancers	Fetal Intestine Large	intestine
24	chr6:113755000-113755600	Flanking Active TSS	A549	lung
25	chr6:113755200-113755800	Enhancers	Hela-S3	cervix
26	chr6:113755200-113756400	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr6:113755200-113756800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:113755400-113755800	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr6:113755400-113757000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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