Variant report

Variant	rs71491792
Chromosome Location	chr9:104211482-104211483
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	chr9:104211440-104211590	GM12873	blood:	n/a	chr9:104211501-104211514
2	CTCF	chr9:104211420-104211570	HRPEpiC	eye:	n/a	chr9:104211501-104211514
3	PAX5	chr9:104211391-104211698	GM12891	blood:	n/a	n/a
4	TCF12	chr9:104211383-104211579	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr9:104211420-104211570	HMEC	breast:	n/a	chr9:104211501-104211514
6	CTCF	chr9:104211460-104211610	NHDF-neo	bronchial:	n/a	chr9:104211501-104211514
7	CTCF	chr9:104211440-104211590	GM12864	blood:	n/a	chr9:104211501-104211514
8	TAF1	chr9:104211407-104211964	H1-hESC	embryonic stem cell:	n/a	n/a
9	RAD21	chr9:104211366-104211971	A549	lung:	n/a	chr9:104211506-104211520 chr9:104211808-104211817
10	CTCF	chr9:104211290-104212054	K562	blood:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
11	RAD21	chr9:104211321-104212048	A549	lung:	n/a	chr9:104211506-104211520 chr9:104211808-104211817
12	MAX	chr9:104211382-104211985	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr9:104211420-104211570	HPAF	blood vessel:	n/a	chr9:104211501-104211514
14	CTCF	chr9:104211480-104211630	GM12869	blood:	n/a	chr9:104211501-104211514
15	CTCF	chr9:104211390-104211901	Spleen_OC	spleen:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
16	RCOR1	chr9:104211388-104211863	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr9:104211372-104211942	MCF-7	breast:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
18	ZKSCAN1	chr9:104211364-104211889	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr9:104211390-104211966	T-47D	breast:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
20	RCOR1	chr9:104211383-104211967	K562	blood:	n/a	n/a
21	CTCF	chr9:104211374-104211946	A549	lung:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
22	CTCF	chr9:104211400-104211550	MCF-7	breast:	n/a	chr9:104211501-104211514
23	MAX	chr9:104211375-104211954	ECC-1	luminal epithelium:	n/a	n/a
24	CTCF	chr9:104211480-104211630	GM12867	blood:	n/a	chr9:104211501-104211514
25	RAD21	chr9:104211374-104211660	K562	blood:	n/a	chr9:104211506-104211520
26	RAD21	chr9:104211419-104211574	GM12878	blood:	n/a	chr9:104211506-104211520
27	MAX	chr9:104211322-104211966	K562	blood:	n/a	n/a
28	UBTF	chr9:104211423-104211967	K562	blood:	n/a	n/a
29	CTCF	chr9:104211440-104211590	HPF	lung:	n/a	chr9:104211501-104211514
30	CTCF	chr9:104211379-104211928	H1-hESC	embryonic stem cell:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
31	MYC	chr9:104211396-104212063	K562	blood:	n/a	n/a
32	CTCF	chr9:104211440-104211590	HCFaa	heart:	n/a	chr9:104211501-104211514
33	HDAC2	chr9:104211345-104212060	MCF-7	breast:	n/a	n/a
34	MXI1	chr9:104211422-104211955	H1-hESC	embryonic stem cell:	n/a	n/a
35	PAX5	chr9:104211402-104211580	GM12892	blood:	n/a	n/a
36	CTCF	chr9:104211480-104211630	HEEpiC	esophagus:	n/a	chr9:104211501-104211514
37	CTCF	chr9:104211440-104211590	HMF	breast:	n/a	chr9:104211501-104211514
38	JUND	chr9:104211387-104211918	H1-hESC	embryonic stem cell:	n/a	chr9:104211404-104211413
39	CTCF	chr9:104211420-104211570	AG09319	gingival:	n/a	chr9:104211501-104211514
40	MAX	chr9:104211405-104211944	K562	blood:	n/a	n/a
41	MAX	chr9:104211196-104212092	A549	lung:	n/a	n/a
42	CEBPB	chr9:104211419-104211825	Hela-S3	cervix:	n/a	n/a
43	TBP	chr9:104211443-104211896	K562	blood:	n/a	n/a
44	CTCF	chr9:104211404-104211620	LNCaP	prostate:	n/a	chr9:104211501-104211514
45	CTCF	chr9:104211420-104211570	Caco-2	colon:	n/a	chr9:104211501-104211514
46	POLR2A	chr9:104211456-104211879	H1-hESC	embryonic stem cell:	n/a	n/a
47	YY1	chr9:104211386-104211811	H1-hESC	embryonic stem cell:	n/a	chr9:104211490-104211504 chr9:104211494-104211508
48	ZNF143	chr9:104211358-104211951	K562	blood:	n/a	chr9:104211494-104211504 chr9:104211556-104211574
49	BRCA1	chr9:104211448-104211877	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr9:104211440-104211590	HUVEC	blood vessel:	n/a	chr9:104211501-104211514

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
ENSG00000136870	Chromatin interaction
ENSG00000136897	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10123064	1.00[AFR][1000 genomes]
rs10989500	1.00[AFR][1000 genomes]
rs10989507	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10989508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10989509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10989510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10989511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10989513	0.86[EUR][1000 genomes]
rs10989514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10989517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12337537	1.00[AFR][1000 genomes]
rs13283255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13284199	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13289803	1.00[AFR][1000 genomes]
rs13291205	1.00[AFR][1000 genomes]
rs13292387	1.00[AFR][1000 genomes]
rs13293022	1.00[AFR][1000 genomes]
rs13293668	0.81[EUR][1000 genomes]
rs13297805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17186534	1.00[AFR][1000 genomes]
rs17186933	1.00[AFR][1000 genomes]
rs17772514	1.00[AFR][1000 genomes]
rs17772612	1.00[AFR][1000 genomes]
rs17772672	1.00[AFR][1000 genomes]
rs17772869	1.00[AFR][1000 genomes]
rs17773076	1.00[AFR][1000 genomes]
rs1929492	1.00[AFR][1000 genomes]
rs34160569	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34664558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34808473	0.85[EUR][1000 genomes]
rs35772088	1.00[AFR][1000 genomes]
rs41310087	1.00[AFR][1000 genomes]
rs45455902	1.00[AFR][1000 genomes]
rs954738	1.00[AFR][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:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104210800-104211600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
2	chr9:104210800-104211600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
3	chr9:104210800-104211600	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr9:104210800-104211800	Active TSS	Liver	Liver
5	chr9:104210800-104211800	Active TSS	K562	blood
6	chr9:104210800-104212000	Active TSS	Hela-S3	cervix
7	chr9:104211000-104211600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:104211000-104211800	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr9:104211000-104211800	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr9:104211000-104211800	Active TSS	Brain Anterior Caudate	brain
11	chr9:104211000-104211800	Active TSS	Duodenum Mucosa	Duodenum
12	chr9:104211000-104211800	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr9:104211000-104212000	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr9:104211000-104212000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:104211000-104212000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr9:104211000-104212000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:104211000-104212000	Enhancers	Fetal Heart	heart
18	chr9:104211000-104212200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr9:104211000-104212200	Active TSS	A549	lung
20	chr9:104211200-104211600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr9:104211200-104211600	Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr9:104211200-104211800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:104211200-104211800	Bivalent/Poised TSS	Primary B cells from cord blood	blood
24	chr9:104211200-104211800	Active TSS	Psoas Muscle	Psoas
25	chr9:104211200-104212000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr9:104211200-104212000	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr9:104211200-104212200	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr9:104211400-104211600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr9:104211400-104211600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
30	chr9:104211400-104211600	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
31	chr9:104211400-104211600	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr9:104211400-104211600	Bivalent/Poised TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr9:104211400-104211600	Bivalent/Poised TSS	Primary T killer naive cells fromperipheralblood	blood
34	chr9:104211400-104211600	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
35	chr9:104211400-104211600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr9:104211400-104211600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr9:104211400-104211600	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
38	chr9:104211400-104211600	Active TSS	Adipose Nuclei	Adipose
39	chr9:104211400-104211600	Active TSS	Esophagus	oesophagus
40	chr9:104211400-104211600	Bivalent/Poised TSS	Fetal Brain Female	brain
41	chr9:104211400-104211600	Active TSS	Fetal Muscle Leg	muscle
42	chr9:104211400-104211600	Bivalent Enhancer	Fetal Thymus	thymus
43	chr9:104211400-104211600	Active TSS	Lung	lung
44	chr9:104211400-104211600	Active TSS	Placenta Amnion	Placenta Amnion
45	chr9:104211400-104211600	Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr9:104211400-104211600	Active TSS	Stomach Smooth Muscle	stomach
47	chr9:104211400-104211600	Active TSS	HMEC	breast
48	chr9:104211400-104211800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr9:104211400-104211800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr9:104211400-104211800	Active TSS	H9 Cell Line	embryonic stem cell

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