Variant report

Variant	rs34154070
Chromosome Location	chr6:143997227-143997228
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	NR3C1	chr6:143997098-143997427	ECC-1	luminal epithelium:	n/a	n/a
2	CEBPB	chr6:143996963-143997635	ECC-1	luminal epithelium:	n/a	chr6:143997291-143997304 chr6:143997291-143997302 chr6:143997293-143997304
3	GATA3	chr6:143997022-143997491	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr6:143997072-143997504	ECC-1	luminal epithelium:	n/a	n/a
5	JUND	chr6:143997062-143997646	T-47D	breast:	n/a	n/a
6	EP300	chr6:143997081-143997519	Hela-S3	cervix:	n/a	chr6:143997495-143997509
7	FOS	chr6:143997143-143997422	MCF10A-Er-Src	breast:	n/a	n/a
8	GATA3	chr6:143997208-143997419	MCF-7	breast:	n/a	n/a
9	FOS	chr6:143997187-143997412	MCF10A-Er-Src	breast:	n/a	n/a
10	FOXA1	chr6:143997097-143997363	T-47D	breast:	n/a	n/a
11	GATA3	chr6:143997031-143997557	T-47D	breast:	n/a	n/a
12	STAT3	chr6:143997119-143997485	MCF10A-Er-Src	breast:	n/a	n/a
13	FOXA1	chr6:143997165-143997897	HepG2	liver:	n/a	chr6:143997677-143997689 chr6:143997681-143997693
14	TEAD4	chr6:143996961-143997524	ECC-1	luminal epithelium:	n/a	n/a
15	TCF7L2	chr6:143997174-143997773	Hela-S3	cervix:	n/a	n/a
16	FOS	chr6:143997142-143997507	MCF10A-Er-Src	breast:	n/a	n/a
17	GATA3	chr6:143997032-143997609	SK-N-SH	brain:	n/a	n/a
18	CEBPB	chr6:143997060-143997803	Hela-S3	cervix:	n/a	chr6:143997291-143997304 chr6:143997291-143997302 chr6:143997293-143997304
19	CEBPB	chr6:143997210-143997417	K562	blood:	n/a	chr6:143997291-143997304 chr6:143997291-143997302 chr6:143997293-143997304
20	TCF12	chr6:143997077-143997686	ECC-1	luminal epithelium:	n/a	n/a
21	FOXA1	chr6:143997143-143997493	T-47D	breast:	n/a	n/a
22	NFIC	chr6:143996895-143997909	ECC-1	luminal epithelium:	n/a	n/a
23	JUND	chr6:143997016-143997541	T-47D	breast:	n/a	n/a
24	RCOR1	chr6:143997122-143997433	Hela-S3	cervix:	n/a	n/a
25	CEBPB	chr6:143997065-143997539	MCF-7	breast:	n/a	chr6:143997291-143997304 chr6:143997291-143997302 chr6:143997293-143997304
26	EP300	chr6:143997038-143997514	T-47D	breast:	n/a	chr6:143997495-143997509
27	CEBPB	chr6:143997184-143997457	A549	lung:	n/a	chr6:143997291-143997304 chr6:143997291-143997302 chr6:143997293-143997304
28	NR2F2	chr6:143997096-143997639	MCF-7	breast:	n/a	n/a
29	POLR2A	chr6:143996988-143997466	MCF10A-Er-Src	breast:	n/a	n/a
30	ELF1	chr6:143996956-143997607	MCF-7	breast:	n/a	n/a
31	JUND	chr6:143996970-143997595	MCF-7	breast:	n/a	n/a
32	NFIC	chr6:143996965-143997562	ECC-1	luminal epithelium:	n/a	n/a
33	GATA3	chr6:143996915-143997819	MCF-7	breast:	n/a	n/a
34	CEBPB	chr6:143997025-143997582	ECC-1	luminal epithelium:	n/a	chr6:143997291-143997304 chr6:143997291-143997302 chr6:143997293-143997304
35	SP1	chr6:143997099-143997552	A549	lung:	n/a	n/a
36	FOS	chr6:143997144-143997473	MCF10A-Er-Src	breast:	n/a	n/a
37	MYC	chr6:143997144-143997387	MCF10A-Er-Src	breast:	n/a	n/a
38	MYC	chr6:143997062-143997523	MCF10A-Er-Src	breast:	n/a	n/a
39	MAX	chr6:143997001-143997536	ECC-1	luminal epithelium:	n/a	n/a
40	TCF7L2	chr6:143997065-143997382	PANC-1	pancreas:	n/a	n/a
41	CEBPB	chr6:143997147-143997422	H1-hESC	embryonic stem cell:	n/a	chr6:143997291-143997304 chr6:143997291-143997302 chr6:143997293-143997304
42	CEBPB	chr6:143997041-143997643	MCF-7	breast:	n/a	chr6:143997291-143997304 chr6:143997291-143997302 chr6:143997293-143997304
43	RAD21	chr6:143997004-143997466	ECC-1	luminal epithelium:	n/a	n/a
44	FOXA1	chr6:143997111-143997451	ECC-1	luminal epithelium:	n/a	n/a
45	GATA3	chr6:143996964-143997652	MCF-7	breast:	n/a	n/a
46	TEAD4	chr6:143997063-143997468	ECC-1	luminal epithelium:	n/a	n/a
47	CEBPB	chr6:143997032-143997592	A549	lung:	n/a	chr6:143997291-143997304 chr6:143997291-143997302 chr6:143997293-143997304
48	FOXM1	chr6:143996869-143998145	ECC-1	luminal epithelium:	n/a	n/a
49	STAT3	chr6:143997145-143997460	MCF10A-Er-Src	breast:	n/a	n/a
50	TCF7L2	chr6:143997125-143997561	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:143994808..143997283-chr6:143999209..144001887,3	MCF-7	breast:

Variant related genes	Relation type
PHACTR2	TF binding region
ENSG00000112419	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs13192982	1.00[ASN][1000 genomes]
rs13195247	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13200953	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13210200	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13214849	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1856391	1.00[ASN][1000 genomes]
rs34549423	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34656252	1.00[ASN][1000 genomes]
rs35907844	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36155996	1.00[ASN][1000 genomes]
rs3924970	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71564441	1.00[ASN][1000 genomes]
rs71564444	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71564446	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9390114	1.00[ASN][1000 genomes]
rs9496711	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	esv2758084	chr6:143916621-144079976	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759476	chr6:143916621-144079976	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1032369	chr6:143925374-144007513	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv604805	chr6:143930404-144005949	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143994000-143997800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr6:143994000-143998800	Enhancers	Hela-S3	cervix
3	chr6:143994200-143997400	Enhancers	H9 Cell Line	embryonic stem cell
4	chr6:143994200-143997600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:143994200-143997800	Enhancers	H1 Cell Line	embryonic stem cell
6	chr6:143994200-143998000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:143994200-143998000	Enhancers	Fetal Kidney	kidney
8	chr6:143994200-143998000	Enhancers	NHDF-Ad	bronchial
9	chr6:143994200-143998000	Enhancers	NHLF	lung
10	chr6:143994200-143998200	Enhancers	HMEC	breast
11	chr6:143994200-143998400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr6:143994200-143998600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:143994200-143998600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr6:143994200-143998600	Enhancers	HepG2	liver
15	chr6:143994200-143999000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:143994400-143997600	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr6:143994600-143999000	Weak transcription	Lung	lung
18	chr6:143994800-143997400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:143994800-143997400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr6:143994800-143999000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:143995000-143998800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:143995200-143998000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:143995200-143998400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:143995200-143998600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:143995400-143997400	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr6:143995400-143997800	Enhancers	Placenta Amnion	Placenta Amnion
27	chr6:143995400-143998200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:143995400-143998800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr6:143995600-143998600	Enhancers	Fetal Intestine Small	intestine
30	chr6:143995600-143998600	Enhancers	HUVEC	blood vessel
31	chr6:143995800-143998400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:143995800-143998600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr6:143995800-143998600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr6:143995800-143998800	Weak transcription	HSMM	muscle
35	chr6:143995800-143998800	Weak transcription	K562	blood
36	chr6:143996000-143997600	Weak transcription	Aorta	Aorta
37	chr6:143996000-143998400	Enhancers	NHEK	skin
38	chr6:143996000-143998600	Weak transcription	Fetal Heart	heart
39	chr6:143996000-143998600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr6:143996000-143998600	Weak transcription	NH-A	brain
41	chr6:143996000-143998800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr6:143996200-143998600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:143996200-143998800	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr6:143996200-143998800	Weak transcription	Ovary	ovary
45	chr6:143996200-143999000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:143996200-143999000	Weak transcription	Esophagus	oesophagus
47	chr6:143996200-143999000	Weak transcription	Pancreas	Pancrea
48	chr6:143996200-143999000	Weak transcription	Small Intestine	intestine
49	chr6:143996400-143997600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr6:143996400-143998400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

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