Variant report

Variant	rs572824
Chromosome Location	chr6:33547159-33547160
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:33544423-33548349	GM12878	blood:	n/a	n/a
2	RUNX3	chr6:33546961-33547250	GM12878	blood:	n/a	n/a
3	PAX5	chr6:33546971-33547273	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:33547134-33547449	GM12892	blood:	n/a	n/a
5	EGR1	chr6:33547150-33547533	K562	blood:	n/a	n/a
6	CEBPB	chr6:33546950-33547246	K562	blood:	n/a	n/a
7	REST	chr6:33547098-33547600	K562	blood:	n/a	chr6:33547316-33547329
8	NR2F2	chr6:33547114-33548401	K562	blood:	n/a	n/a
9	CEBPB	chr6:33547032-33547169	Hela-S3	cervix:	n/a	n/a
10	YY1	chr6:33547069-33547336	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:33547107-33547549	GM12878	blood:	n/a	n/a
12	RUNX3	chr6:33546889-33547469	GM12878	blood:	n/a	n/a
13	ELF1	chr6:33547137-33548229	GM12878	blood:	n/a	chr6:33547405-33547418
14	PAX5	chr6:33546943-33547365	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:33547146-33547271	GM12878	blood:	n/a	n/a
16	MTA3	chr6:33547014-33547685	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33381203..33384118-chr6:33546265..33549089,2	K562	blood:
2	chr6:33391848..33395045-chr6:33544542..33547433,3	MCF-7	breast:
3	chr6:33545816..33547496-chr6:33675270..33677360,2	K562	blood:
4	chr6:33420831..33423204-chr6:33545367..33547352,2	MCF-7	breast:
5	chr6:33546298..33549471-chr6:33550091..33553469,5	K562	blood:
6	chr6:33541749..33544429-chr6:33546198..33547784,2	MCF-7	breast:
7	chr6:33420326..33423381-chr6:33545501..33547721,3	MCF-7	breast:
8	chr6:33546546..33549178-chr6:33588334..33590241,2	K562	blood:

No data

Variant related genes	Relation type
GGNBP1	TF binding region
ENSG00000112511	Chromatin interaction
ENSG00000096433	Chromatin interaction
ENSG00000213588	Chromatin interaction
ENSG00000204188	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1536042	1.00[ASN][1000 genomes]
rs16869178	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1705000	1.00[ASN][1000 genomes]
rs1755041	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755042	1.00[ASN][1000 genomes]
rs1755054	1.00[ASN][1000 genomes]
rs1794686	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1794688	1.00[ASN][1000 genomes]
rs2068236	1.00[ASN][1000 genomes]
rs2147655	1.00[ASN][1000 genomes]
rs2395451	1.00[ASN][1000 genomes]
rs4711333	1.00[ASN][1000 genomes]
rs4711334	1.00[ASN][1000 genomes]
rs4713647	1.00[ASN][1000 genomes]
rs4713652	1.00[ASN][1000 genomes]
rs472990	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480568	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485623	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535584	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542056	1.00[ASN][1000 genomes]
rs542725	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549719	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55700437	1.00[ASN][1000 genomes]
rs557559	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs560218	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs561276	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59572422	1.00[ASN][1000 genomes]
rs61687548	1.00[ASN][1000 genomes]
rs6900438	1.00[ASN][1000 genomes]
rs6906810	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928341	1.00[ASN][1000 genomes]
rs71536195	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752930	1.00[ASN][1000 genomes]
rs7757391	1.00[ASN][1000 genomes]
rs7757722	1.00[ASN][1000 genomes]
rs7759154	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775313	1.00[ASN][1000 genomes]
rs806604	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368770	1.00[ASN][1000 genomes]
rs9689326	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462896	chr6:33534880-33588147	Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv602833	chr6:33534880-33588147	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885770	chr6:33543409-33614127	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33539200-33547200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:33543400-33547200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:33543600-33547200	Weak transcription	HSMMtube	muscle
4	chr6:33544000-33547200	Weak transcription	Ovary	ovary
5	chr6:33544600-33547400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
6	chr6:33544600-33547600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr6:33544800-33548000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:33545200-33547200	Active TSS	Rectal Smooth Muscle	rectum
9	chr6:33545400-33547200	Weak transcription	Aorta	Aorta
10	chr6:33545400-33547200	Enhancers	Pancreas	Pancrea
11	chr6:33545400-33547800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:33545600-33547600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr6:33545600-33548200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
14	chr6:33545800-33547600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr6:33545800-33547800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr6:33546000-33547200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr6:33546000-33547200	Enhancers	Fetal Heart	heart
18	chr6:33546000-33547400	Flanking Active TSS	Fetal Thymus	thymus
19	chr6:33546000-33547600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
20	chr6:33546000-33548000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr6:33546000-33548200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:33546000-33548200	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr6:33546000-33548200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:33546000-33548400	Flanking Active TSS	Primary B cells from peripheral blood	blood
25	chr6:33546200-33547200	Enhancers	Brain Substantia Nigra	brain
26	chr6:33546200-33547200	Flanking Active TSS	HepG2	liver
27	chr6:33546200-33547400	Flanking Active TSS	Right Ventricle	heart
28	chr6:33546200-33547600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr6:33546200-33547800	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr6:33546200-33547800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr6:33546200-33548000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:33546200-33548000	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr6:33546200-33548000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:33546200-33548000	Active TSS	Small Intestine	intestine
35	chr6:33546200-33548200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:33546200-33548200	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr6:33546200-33548200	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr6:33546200-33548200	Active TSS	Duodenum Mucosa	Duodenum
39	chr6:33546400-33547200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr6:33546400-33547200	Enhancers	Liver	Liver
41	chr6:33546400-33547400	Flanking Active TSS	Dnd41	blood
42	chr6:33546400-33547600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr6:33546400-33547600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:33546400-33547600	Flanking Active TSS	Brain Hippocampus Middle	brain
45	chr6:33546400-33547600	Enhancers	Fetal Brain Male	brain
46	chr6:33546400-33547600	Flanking Active TSS	Stomach Smooth Muscle	stomach
47	chr6:33546400-33548000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr6:33546400-33548000	Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr6:33546400-33548200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:33546400-33548200	Active TSS	A549	lung

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