Variant report

Variant	rs2294231
Chromosome Location	chr6:113754404-113754405
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	CEBPB	chr6:113753887-113755234	Hela-S3	cervix:	n/a	chr6:113754871-113754882 chr6:113754869-113754882
2	BCL3	chr6:113754122-113754485	GM12878	blood:	n/a	n/a
3	FOSL2	chr6:113753947-113755124	A549	lung:	n/a	chr6:113754145-113754157
4	ESR1	chr6:113753920-113755353	T-47D	breast:	n/a	n/a
5	ESR1	chr6:113753958-113755288	T-47D	breast:	n/a	n/a
6	ESR1	chr6:113753996-113755245	T-47D	breast:	n/a	n/a
7	FOXA1	chr6:113754019-113755372	T-47D	breast:	n/a	n/a
8	SIN3AK20	chr6:113754259-113755430	MCF-7	breast:	n/a	n/a
9	CEBPB	chr6:113753916-113755067	A549	lung:	n/a	chr6:113754871-113754882 chr6:113754869-113754882
10	ESR1	chr6:113753958-113755298	T-47D	breast:	n/a	n/a
11	EP300	chr6:113753838-113755270	A549	lung:	n/a	chr6:113755150-113755160 chr6:113753975-113753989 chr6:113753976-113753984 chr6:113753873-113753887
12	RAD21	chr6:113754375-113755280	MCF-7	breast:	n/a	n/a
13	TCF12	chr6:113754328-113755177	MCF-7	breast:	n/a	n/a
14	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
15	CEBPB	chr6:113753888-113754477	MCF-7	breast:	n/a	n/a
16	FOXA2	chr6:113754100-113754441	A549	lung:	n/a	n/a
17	GATA3	chr6:113753929-113755159	A549	lung:	n/a	n/a
18	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
19	FOXA1	chr6:113753961-113755419	T-47D	breast:	n/a	n/a
20	FOS	chr6:113753894-113755008	MCF10A-Er-Src	breast:	n/a	chr6:113754145-113754157 chr6:113753918-113753926
21	GATA3	chr6:113753876-113755661	MCF-7	breast:	n/a	chr6:113755373-113755389 chr6:113755377-113755384 chr6:113755377-113755384 chr6:113755375-113755387 chr6:113755377-113755384
22	CEBPB	chr6:113753928-113755259	IMR90	lung:	n/a	chr6:113754871-113754882 chr6:113754869-113754882
23	RFX5	chr6:113754180-113755289	Hela-S3	cervix:	n/a	n/a
24	FOXA2	chr6:113753926-113755283	A549	lung:	n/a	n/a
25	NR2F2	chr6:113753989-113755447	MCF-7	breast:	n/a	n/a
26	BCL3	chr6:113753888-113755123	A549	lung:	n/a	n/a
27	CHD2	chr6:113754031-113755097	Hela-S3	cervix:	n/a	n/a
28	EP300	chr6:113754103-113755353	T-47D	breast:	n/a	chr6:113755150-113755160
29	EP300	chr6:113753817-113755479	T-47D	breast:	n/a	chr6:113755150-113755160 chr6:113753975-113753989 chr6:113753976-113753984 chr6:113753873-113753887
30	FOSL2	chr6:113754341-113755361	MCF-7	breast:	n/a	n/a
31	GATA3	chr6:113753950-113755449	T-47D	breast:	n/a	chr6:113755373-113755389 chr6:113755377-113755384 chr6:113755377-113755384 chr6:113755375-113755387 chr6:113755377-113755384
32	CEBPB	chr6:113753852-113755255	A549	lung:	n/a	chr6:113754871-113754882 chr6:113754869-113754882
33	TCF12	chr6:113754049-113755658	MCF-7	breast:	n/a	n/a
34	HDAC2	chr6:113754386-113755290	MCF-7	breast:	n/a	n/a
35	SMC3	chr6:113754160-113755296	Hela-S3	cervix:	n/a	n/a
36	REST	chr6:113753878-113755061	A549	lung:	n/a	n/a
37	SIN3AK20	chr6:113753876-113755591	MCF-7	breast:	n/a	n/a
38	FOXM1	chr6:113753798-113755513	MCF-7	breast:	n/a	n/a
39	JUND	chr6:113753939-113755483	T-47D	breast:	n/a	chr6:113754145-113754157
40	SP1	chr6:113753904-113755294	A549	lung:	n/a	n/a
41	SP1	chr6:113753811-113755252	A549	lung:	n/a	n/a
42	ESR1	chr6:113754373-113755275	T-47D	breast:	n/a	n/a
43	JUND	chr6:113754276-113755469	T-47D	breast:	n/a	n/a
44	ESR1	chr6:113754380-113755304	T-47D	breast:	n/a	n/a
45	TCF12	chr6:113753707-113755418	A549	lung:	n/a	n/a
46	GATA3	chr6:113753995-113755569	T-47D	breast:	n/a	chr6:113755373-113755389 chr6:113755377-113755384 chr6:113755377-113755384 chr6:113755375-113755387 chr6:113755377-113755384
47	EP300	chr6:113753891-113755256	Hela-S3	cervix:	n/a	chr6:113755150-113755160 chr6:113753975-113753989 chr6:113753976-113753984
48	GATA3	chr6:113754069-113755578	MCF-7	breast:	n/a	chr6:113755373-113755389 chr6:113755377-113755384 chr6:113755377-113755384 chr6:113755375-113755387 chr6:113755377-113755384
49	ZNF217	chr6:113753995-113755366	MCF-7	breast:	n/a	n/a
50	EP300	chr6:113753973-113755384	MCF-7	breast:	n/a	chr6:113755150-113755160 chr6:113753975-113753989 chr6:113753976-113753984

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:113753088..113757268-chr6:113951584..113954499,3	MCF-7	breast:
2	chr6:113753712..113755714-chr6:114178275..114180113,2	MCF-7	breast:

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

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10080444	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10080706	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1033390	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1033391	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10457266	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10484459	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10872095	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10872097	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11153417	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11153418	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12203134	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12214468	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[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];0.97[ASN][1000 genomes]
rs2049924	0.82[CHD][hapmap]
rs2092086	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2092087	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2103538	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2142641	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2179118	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2348304	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4380793	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4435975	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4945948	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5001721	0.85[ASN][1000 genomes]
rs6568791	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6914474	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6914499	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6938194	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs764733	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs764734	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs766329	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs766330	0.85[ASN][1000 genomes]
rs7738898	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7758769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7759869	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7771550	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7771810	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7772108	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7772790	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7776236	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs909542	0.87[CHD][hapmap]
rs9320453	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9320455	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9320456	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9320457	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9320458	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9481352	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9481355	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9481356	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9481357	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9481358	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9481359	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9481360	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9481361	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9481365	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9488184	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9488187	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9488189	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9488190	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9488191	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9488195	0.86[EUR][1000 genomes];0.91[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
rs2294231	RWDD1	cis	cerebellum	SCAN
rs2294231	RFPL4B	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:113753000-113755800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr6:113753200-113754800	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr6:113753400-113755800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:113753600-113755400	Enhancers	Liver	Liver
5	chr6:113753600-113755400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr6:113753600-113755600	Enhancers	Primary B cells from cord blood	blood
7	chr6:113753600-113755600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:113753600-113755800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:113753600-113755800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:113753600-113755800	Enhancers	NHDF-Ad	bronchial
11	chr6:113753600-113755800	Enhancers	NHLF	lung
12	chr6:113753600-113756200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:113753600-113756600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:113753600-113756800	Enhancers	Osteobl	bone
15	chr6:113753800-113754600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:113753800-113755200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:113753800-113755400	Enhancers	Muscle Satellite Cultured Cells	--
18	chr6:113753800-113756000	Enhancers	Placenta	Placenta
19	chr6:113753800-113756200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:113753800-113756600	Enhancers	Fetal Lung	lung
21	chr6:113754000-113755200	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr6:113754000-113755800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr6:113754200-113755000	Enhancers	HepG2	liver
24	chr6:113754200-113755200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:113754200-113755200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:113754200-113755200	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr6:113754200-113755200	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr6:113754200-113755200	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr6:113754200-113755200	Enhancers	Stomach Mucosa	stomach
30	chr6:113754200-113755200	Enhancers	NHEK	skin
31	chr6:113754200-113755600	Enhancers	Adipose Nuclei	Adipose
32	chr6:113754200-113755600	Enhancers	HMEC	breast
33	chr6:113754200-113755800	Enhancers	Fetal Intestine Small	intestine
34	chr6:113754200-113755800	Enhancers	Ovary	ovary
35	chr6:113754200-113756000	Enhancers	Colon Smooth Muscle	Colon
36	chr6:113754200-113756800	Enhancers	Fetal Stomach	stomach
37	chr6:113754400-113754600	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr6:113754400-113754600	Flanking Active TSS	A549	lung
39	chr6:113754400-113755000	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr6:113754400-113755200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:113754400-113755200	Flanking Active TSS	Hela-S3	cervix
42	chr6:113754400-113755600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr6:113754400-113755600	Enhancers	Fetal Intestine Large	intestine

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