Variant report

Variant	rs35601036
Chromosome Location	chr6:54711096-54711097
allele	C/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	POLR2A	chr6:54711091-54711664	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr6:54710974-54713675	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr6:54710993-54712194	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr6:54710926-54712518	HCT-116	colon:	n/a	n/a
5	SIN3AK20	chr6:54710924-54711875	MCF-7	breast:	n/a	n/a
6	STAT1	chr6:54711042-54713361	Hela-S3	cervix:	n/a	chr6:54712038-54712045 chr6:54712078-54712087 chr6:54712079-54712088 chr6:54711525-54711537 chr6:54712079-54712087 chr6:54713023-54713037 chr6:54712073-54712093 chr6:54711520-54711532 chr6:54711993-54712005 chr6:54712073-54712093 chr6:54713026-54713034 chr6:54712077-54712088 chr6:54713165-54713173
7	SMARCC1	chr6:54711045-54713431	Hela-S3	cervix:	n/a	n/a
8	MAX	chr6:54710957-54713446	Hela-S3	cervix:	n/a	chr6:54711427-54711437
9	TCF12	chr6:54710972-54712270	ECC-1	luminal epithelium:	n/a	n/a
10	SMARCB1	chr6:54710981-54712318	Hela-S3	cervix:	n/a	n/a
11	HDAC2	chr6:54711036-54712299	MCF-7	breast:	n/a	chr6:54711294-54711308
12	CTBP2	chr6:54711055-54712274	H1-hESC	embryonic stem cell:	n/a	n/a
13	RAD21	chr6:54710988-54712411	Hela-S3	cervix:	n/a	chr6:54711672-54711686
14	SIN3AK20	chr6:54710850-54713528	MCF-7	breast:	n/a	n/a
15	REST	chr6:54711052-54711667	MCF-7	breast:	n/a	chr6:54711484-54711504 chr6:54711209-54711218
16	MXI1	chr6:54711059-54713305	Hela-S3	cervix:	n/a	n/a
17	YY1	chr6:54710903-54711377	H1-hESC	embryonic stem cell:	n/a	n/a
18	RCOR1	chr6:54711049-54712070	Hela-S3	cervix:	n/a	n/a
19	TAF1	chr6:54710999-54712164	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr6:54711064-54713478	MCF10A-Er-Src	breast:	n/a	n/a
21	KAP1	chr6:54710888-54712803	HEK293	kidney:	n/a	n/a
22	TAF1	chr6:54711003-54712273	MCF-7	breast:	n/a	n/a
23	POLR2A	chr6:54710891-54712384	MCF-7	breast:	n/a	n/a
24	ZNF263	chr6:54710951-54712438	HEK293-T-REx	kidney:	n/a	n/a
25	POLR2A	chr6:54711082-54711775	HCT-116	colon:	n/a	n/a
26	MAX	chr6:54711052-54712166	H1-hESC	embryonic stem cell:	n/a	chr6:54711427-54711437
27	MAZ	chr6:54711007-54712408	Hela-S3	cervix:	n/a	chr6:54711427-54711437
28	CHD2	chr6:54711046-54711575	H1-hESC	embryonic stem cell:	n/a	chr6:54711229-54711239
29	ELF1	chr6:54710934-54711748	MCF-7	breast:	n/a	n/a
30	ZBTB7A	chr6:54710869-54712201	ECC-1	luminal epithelium:	n/a	chr6:54711709-54711717
31	GTF2F1	chr6:54710933-54713386	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr6:54710921-54712326	MCF-7	breast:	n/a	n/a
33	MAX	chr6:54710873-54712290	ECC-1	luminal epithelium:	n/a	chr6:54711427-54711437
34	RFX5	chr6:54711009-54712070	Hela-S3	cervix:	n/a	n/a
35	RAD21	chr6:54711001-54711686	H1-hESC	embryonic stem cell:	n/a	chr6:54711672-54711686
36	POLR2A	chr6:54710340-54713314	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr6:54711045-54711996	ProgFib	skin:	n/a	n/a
38	TCF7L2	chr6:54711075-54713561	Hela-S3	cervix:	n/a	chr6:54713460-54713469
39	MAX	chr6:54710934-54712257	ECC-1	luminal epithelium:	n/a	chr6:54711427-54711437
40	TBP	chr6:54711053-54711675	H1-hESC	embryonic stem cell:	n/a	n/a
41	BACH1	chr6:54710981-54711290	H1-hESC	embryonic stem cell:	n/a	n/a
42	MAX	chr6:54710930-54712220	MCF-7	breast:	n/a	chr6:54711427-54711437
43	SIN3A	chr6:54711023-54712103	H1-hESC	embryonic stem cell:	n/a	chr6:54711584-54711597
44	ZBTB7A	chr6:54710945-54712327	ECC-1	luminal epithelium:	n/a	chr6:54711709-54711717
45	SMC3	chr6:54711003-54713437	Hela-S3	cervix:	n/a	n/a
46	JUND	chr6:54710983-54711687	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr6:54710248-54714679	MCF-7	breast:	n/a	n/a
48	GATA3	chr6:54711010-54711939	MCF-7	breast:	n/a	chr6:54711293-54711303 chr6:54711565-54711573
49	MAX	chr6:54711008-54711719	H1-hESC	embryonic stem cell:	n/a	chr6:54711427-54711437
50	MAX	chr6:54710959-54711775	MCF-7	breast:	n/a	chr6:54711427-54711437

No.	Distal block	Cell Line	Cell type
1	chr6:54709139..54711220-chr6:54750997..54752618,2	MCF-7	breast:
2	chr6:54556132..54558033-chr6:54708676..54711461,2	MCF-7	breast:
3	chr14:65876592..65878564-chr6:54710365..54711981,2	MCF-7	breast:
4	chr6:54709202..54711186-chr6:54779955..54782595,2	MCF-7	breast:
5	chr6:54633061..54636995-chr6:54710354..54713223,5	MCF-7	breast:

Variant related genes	Relation type
FAM83B	TF binding region
ENSG00000220635	Chromatin interaction
ENSG00000033170	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12196439	1.00[ASN][1000 genomes]
rs12207828	1.00[ASN][1000 genomes]
rs13190743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192654	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13212537	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13218354	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13220607	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395638	1.00[ASN][1000 genomes]
rs1395639	1.00[ASN][1000 genomes]
rs17682062	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239782	1.00[ASN][1000 genomes]
rs239784	1.00[ASN][1000 genomes]
rs239785	1.00[ASN][1000 genomes]
rs34317450	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34784567	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35242257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35332422	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35355591	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35776136	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929628	1.00[ASN][1000 genomes]
rs6930882	1.00[ASN][1000 genomes]
rs6936719	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71560861	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71560863	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71560865	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71560870	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71560871	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71560872	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9464152	1.00[ASN][1000 genomes]
rs9474993	1.00[ASN][1000 genomes]
rs9474994	1.00[ASN][1000 genomes]
rs9474998	1.00[ASN][1000 genomes]
rs9474999	1.00[ASN][1000 genomes]
rs9475000	1.00[ASN][1000 genomes]
rs9475047	1.00[ASN][1000 genomes]
rs9475049	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54709000-54713400	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr6:54709000-54714200	Active TSS	Duodenum Mucosa	Duodenum
3	chr6:54709800-54713400	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr6:54710200-54711200	Flanking Active TSS	HMEC	breast
5	chr6:54710200-54711600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:54710400-54711200	Flanking Active TSS	NHEK	skin
7	chr6:54710400-54713200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr6:54710600-54711200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:54710600-54713800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:54710800-54711200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
11	chr6:54710800-54711400	Flanking Active TSS	Placenta	Placenta
12	chr6:54710800-54711400	Active TSS	Rectal Smooth Muscle	rectum
13	chr6:54710800-54712200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:54710800-54712200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
15	chr6:54710800-54712400	Active TSS	H9 Cell Line	embryonic stem cell
16	chr6:54710800-54712400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
17	chr6:54710800-54712400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:54710800-54712600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
19	chr6:54710800-54712600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
20	chr6:54710800-54712800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:54710800-54713000	Active TSS	Fetal Intestine Small	intestine
22	chr6:54710800-54713000	Active TSS	Right Atrium	heart
23	chr6:54710800-54713600	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr6:54710800-54714400	Active TSS	Colonic Mucosa	Colon
25	chr6:54711000-54711200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
26	chr6:54711000-54711200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:54711000-54711200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
28	chr6:54711000-54711200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:54711000-54711200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr6:54711000-54711200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
31	chr6:54711000-54711200	Bivalent Enhancer	Brain Hippocampus Middle	brain
32	chr6:54711000-54711200	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
33	chr6:54711000-54711200	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:54711000-54711200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
35	chr6:54711000-54711200	Bivalent Enhancer	Fetal Brain Male	brain
36	chr6:54711000-54711200	Bivalent/Poised TSS	Fetal Lung	lung
37	chr6:54711000-54711200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
38	chr6:54711000-54711200	Flanking Bivalent TSS/Enh	Left Ventricle	heart
39	chr6:54711000-54711200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
40	chr6:54711000-54711200	Active TSS	Right Ventricle	heart
41	chr6:54711000-54711200	Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr6:54711000-54711200	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr6:54711000-54711200	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
44	chr6:54711000-54711400	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:54711000-54711400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:54711000-54711400	Bivalent Enhancer	Brain Substantia Nigra	brain
47	chr6:54711000-54711400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
48	chr6:54711000-54711600	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:54711000-54711600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:54711000-54711600	Enhancers	Spleen	Spleen

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