Variant report

Variant	rs34160569
Chromosome Location	chr9:104211733-104211734
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	CTCF	chr9:104211680-104211830	GM12866	blood:	n/a	chr9:104211786-104211802
2	TBP	chr9:104211494-104211938	H1-hESC	embryonic stem cell:	n/a	n/a
3	TAF1	chr9:104211407-104211964	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr9:104211366-104211971	A549	lung:	n/a	chr9:104211506-104211520 chr9:104211808-104211817
5	CTCF	chr9:104211290-104212054	K562	blood:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
6	RAD21	chr9:104211321-104212048	A549	lung:	n/a	chr9:104211506-104211520 chr9:104211808-104211817
7	MAX	chr9:104211382-104211985	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr9:104211700-104211850	HMF	breast:	n/a	chr9:104211786-104211802
9	CTCF	chr9:104211700-104211850	HRPEpiC	eye:	n/a	chr9:104211786-104211802
10	CTCF	chr9:104211390-104211901	Spleen_OC	spleen:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
11	RCOR1	chr9:104211388-104211863	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr9:104211372-104211942	MCF-7	breast:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
13	ZKSCAN1	chr9:104211364-104211889	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr9:104211390-104211966	T-47D	breast:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
15	RCOR1	chr9:104211383-104211967	K562	blood:	n/a	n/a
16	CTCF	chr9:104211720-104211870	HBMEC	blood vessel:	n/a	chr9:104211786-104211802
17	CTCF	chr9:104211374-104211946	A549	lung:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
18	CTCF	chr9:104211660-104211810	SAEC	small airway:	n/a	chr9:104211786-104211802
19	MAX	chr9:104211375-104211954	ECC-1	luminal epithelium:	n/a	n/a
20	RAD21	chr9:104211674-104212030	MCF-7	breast:	n/a	chr9:104211808-104211817
21	MAX	chr9:104211322-104211966	K562	blood:	n/a	n/a
22	UBTF	chr9:104211423-104211967	K562	blood:	n/a	n/a
23	CTCF	chr9:104211379-104211928	H1-hESC	embryonic stem cell:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
24	MYC	chr9:104211396-104212063	K562	blood:	n/a	n/a
25	HDAC2	chr9:104211345-104212060	MCF-7	breast:	n/a	n/a
26	MXI1	chr9:104211422-104211955	H1-hESC	embryonic stem cell:	n/a	n/a
27	JUND	chr9:104211387-104211918	H1-hESC	embryonic stem cell:	n/a	chr9:104211404-104211413
28	CTCF	chr9:104211700-104211850	Hela-S3	cervix:	n/a	chr9:104211786-104211802
29	CTCF	chr9:104211700-104211850	Caco-2	colon:	n/a	chr9:104211786-104211802
30	MAX	chr9:104211405-104211944	K562	blood:	n/a	n/a
31	MAX	chr9:104211196-104212092	A549	lung:	n/a	n/a
32	CTCF	chr9:104211680-104211830	HPF	lung:	n/a	chr9:104211786-104211802
33	CTCF	chr9:104211680-104211830	HEEpiC	esophagus:	n/a	chr9:104211786-104211802
34	CEBPB	chr9:104211419-104211825	Hela-S3	cervix:	n/a	n/a
35	TBP	chr9:104211443-104211896	K562	blood:	n/a	n/a
36	POLR2A	chr9:104211456-104211879	H1-hESC	embryonic stem cell:	n/a	n/a
37	YY1	chr9:104211386-104211811	H1-hESC	embryonic stem cell:	n/a	chr9:104211490-104211504 chr9:104211494-104211508
38	ZNF143	chr9:104211358-104211951	K562	blood:	n/a	chr9:104211494-104211504 chr9:104211556-104211574
39	CTCF	chr9:104211650-104211928	ECC-1	luminal epithelium:	n/a	chr9:104211786-104211802
40	BRCA1	chr9:104211448-104211877	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr9:104211369-104211946	MCF-7	breast:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
42	CTCF	chr9:104211394-104211929	GM19239	blood:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
43	RAD21	chr9:104211388-104211948	K562	blood:	n/a	chr9:104211506-104211520 chr9:104211808-104211817
44	RAD21	chr9:104211337-104212070	ECC-1	luminal epithelium:	n/a	chr9:104211506-104211520 chr9:104211808-104211817
45	CTCF	chr9:104211700-104211850	GM12871	blood:	n/a	chr9:104211786-104211802
46	SP4	chr9:104211601-104211970	H1-hESC	embryonic stem cell:	n/a	n/a
47	YY1	chr9:104211698-104211896	HCT-116	colon:	n/a	n/a
48	CTCF	chr9:104211630-104211905	SK-N-SH_RA	brain:	n/a	chr9:104211786-104211802
49	CHD2	chr9:104211441-104211874	GM12878	blood:	n/a	n/a
50	MAX	chr9:104211424-104211951	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:104160996..104162683-chr9:104210087..104212007,2	K562	blood:
2	chr2:170838366..170838866-chr9:104211065..104211816,2	MCF-7	breast:
3	chr9:104160683..104161236-chr9:104211196..104212187,2	MCF-7	breast:
4	chr9:104211411..104211984-chr9:104329284..104330026,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270982	TF binding region
ENSG00000136897	Chromatin interaction
ENSG00000136870	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10989507	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10989508	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10989509	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10989510	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10989511	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10989513	0.86[EUR][1000 genomes]
rs10989514	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10989517	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13283255	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13284199	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13293668	0.81[EUR][1000 genomes]
rs13297805	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34664558	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34808473	0.85[EUR][1000 genomes]
rs71491792	0.92[AMR][1000 genomes];1.00[EUR][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	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv893626	chr9:104172936-104324545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv614962	chr9:104204614-104240708	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104210800-104211800	Active TSS	Liver	Liver
2	chr9:104210800-104211800	Active TSS	K562	blood
3	chr9:104210800-104212000	Active TSS	Hela-S3	cervix
4	chr9:104211000-104211800	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr9:104211000-104211800	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr9:104211000-104211800	Active TSS	Brain Anterior Caudate	brain
7	chr9:104211000-104211800	Active TSS	Duodenum Mucosa	Duodenum
8	chr9:104211000-104211800	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr9:104211000-104212000	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr9:104211000-104212000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:104211000-104212000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr9:104211000-104212000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr9:104211000-104212000	Enhancers	Fetal Heart	heart
14	chr9:104211000-104212200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:104211000-104212200	Active TSS	A549	lung
16	chr9:104211200-104211800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:104211200-104211800	Bivalent/Poised TSS	Primary B cells from cord blood	blood
18	chr9:104211200-104211800	Active TSS	Psoas Muscle	Psoas
19	chr9:104211200-104212000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:104211200-104212000	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr9:104211200-104212200	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr9:104211400-104211800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:104211400-104211800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:104211400-104211800	Active TSS	H9 Cell Line	embryonic stem cell
25	chr9:104211400-104211800	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr9:104211400-104211800	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr9:104211400-104211800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:104211400-104211800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr9:104211400-104211800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
30	chr9:104211400-104211800	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
31	chr9:104211400-104211800	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr9:104211400-104211800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr9:104211400-104211800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
34	chr9:104211400-104211800	Active TSS	Brain Angular Gyrus	brain
35	chr9:104211400-104211800	Active TSS	Brain Cingulate Gyrus	brain
36	chr9:104211400-104211800	Flanking Active TSS	Brain Germinal Matrix	brain
37	chr9:104211400-104211800	Active TSS	Brain Hippocampus Middle	brain
38	chr9:104211400-104211800	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr9:104211400-104211800	Active TSS	Brain Substantia Nigra	brain
40	chr9:104211400-104211800	Bivalent/Poised TSS	Fetal Stomach	stomach
41	chr9:104211400-104211800	Active TSS	Ovary	ovary
42	chr9:104211400-104211800	Active TSS	Pancreas	Pancrea
43	chr9:104211400-104211800	Active TSS	Rectal Smooth Muscle	rectum
44	chr9:104211400-104211800	Transcr. at gene 5' and 3'	Right Atrium	heart
45	chr9:104211400-104211800	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
46	chr9:104211400-104211800	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr9:104211400-104211800	Bivalent/Poised TSS	Thymus	Thymus
48	chr9:104211400-104211800	Bivalent/Poised TSS	NHEK	skin
49	chr9:104211400-104211800	Active TSS	Osteobl	bone
50	chr9:104211400-104212000	Active TSS	H1 Cell Line	embryonic stem cell

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