Variant report

Variant	rs10989510
Chromosome Location	chr9:104211886-104211887
allele	A/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	TBP	chr9:104211494-104211938	H1-hESC	embryonic stem cell:	n/a	n/a
2	TAF1	chr9:104211407-104211964	H1-hESC	embryonic stem cell:	n/a	n/a
3	RAD21	chr9:104211366-104211971	A549	lung:	n/a	chr9:104211506-104211520 chr9:104211808-104211817
4	CTCF	chr9:104211290-104212054	K562	blood:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
5	RAD21	chr9:104211321-104212048	A549	lung:	n/a	chr9:104211506-104211520 chr9:104211808-104211817
6	MAX	chr9:104211382-104211985	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr9:104211390-104211901	Spleen_OC	spleen:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
8	CTCF	chr9:104211372-104211942	MCF-7	breast:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
9	ZKSCAN1	chr9:104211364-104211889	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr9:104211390-104211966	T-47D	breast:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
11	RCOR1	chr9:104211383-104211967	K562	blood:	n/a	n/a
12	CTCF	chr9:104211374-104211946	A549	lung:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
13	MAX	chr9:104211375-104211954	ECC-1	luminal epithelium:	n/a	n/a
14	RAD21	chr9:104211674-104212030	MCF-7	breast:	n/a	chr9:104211808-104211817
15	MAX	chr9:104211322-104211966	K562	blood:	n/a	n/a
16	UBTF	chr9:104211423-104211967	K562	blood:	n/a	n/a
17	CTCF	chr9:104211379-104211928	H1-hESC	embryonic stem cell:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
18	MYC	chr9:104211396-104212063	K562	blood:	n/a	n/a
19	HDAC2	chr9:104211345-104212060	MCF-7	breast:	n/a	n/a
20	MXI1	chr9:104211422-104211955	H1-hESC	embryonic stem cell:	n/a	n/a
21	JUND	chr9:104211387-104211918	H1-hESC	embryonic stem cell:	n/a	chr9:104211404-104211413
22	MAX	chr9:104211405-104211944	K562	blood:	n/a	n/a
23	MAX	chr9:104211196-104212092	A549	lung:	n/a	n/a
24	TBP	chr9:104211443-104211896	K562	blood:	n/a	n/a
25	ZNF143	chr9:104211358-104211951	K562	blood:	n/a	chr9:104211494-104211504 chr9:104211556-104211574
26	CTCF	chr9:104211650-104211928	ECC-1	luminal epithelium:	n/a	chr9:104211786-104211802
27	CTCF	chr9:104211740-104211890	GM12875	blood:	n/a	chr9:104211786-104211802
28	CTCF	chr9:104211740-104211890	AoAF	blood vessel:	n/a	chr9:104211786-104211802
29	CTCF	chr9:104211369-104211946	MCF-7	breast:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
30	CTCF	chr9:104211394-104211929	GM19239	blood:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
31	RAD21	chr9:104211388-104211948	K562	blood:	n/a	chr9:104211506-104211520 chr9:104211808-104211817
32	RAD21	chr9:104211337-104212070	ECC-1	luminal epithelium:	n/a	chr9:104211506-104211520 chr9:104211808-104211817
33	SP4	chr9:104211601-104211970	H1-hESC	embryonic stem cell:	n/a	n/a
34	YY1	chr9:104211698-104211896	HCT-116	colon:	n/a	n/a
35	CTCF	chr9:104211630-104211905	SK-N-SH_RA	brain:	n/a	chr9:104211786-104211802
36	MAX	chr9:104211424-104211951	Hela-S3	cervix:	n/a	n/a
37	CTCF	chr9:104211390-104211899	Pancreas_OC	pancreas:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
38	SP1	chr9:104211276-104211916	A549	lung:	n/a	chr9:104211531-104211545 chr9:104211535-104211544 chr9:104211536-104211545
39	RAD21	chr9:104211712-104211917	GM12878	blood:	n/a	chr9:104211808-104211817
40	CTCF	chr9:104211667-104211898	LNCaP	prostate:	n/a	chr9:104211786-104211802
41	RAD21	chr9:104211388-104212057	MCF-7	breast:	n/a	chr9:104211506-104211520 chr9:104211808-104211817
42	CTCF	chr9:104211384-104211927	ProgFib	skin:	n/a	chr9:104211501-104211514 chr9:104211786-104211802
43	RAD21	chr9:104211338-104211989	IMR90	lung:	n/a	chr9:104211506-104211520 chr9:104211808-104211817
44	RAD21	chr9:104211197-104212204	HCT-116	colon:	n/a	chr9:104211506-104211520 chr9:104211808-104211817
45	BHLHE40	chr9:104211362-104211952	K562	blood:	n/a	chr9:104211458-104211474 chr9:104211497-104211513 chr9:104211492-104211508
46	UBTF	chr9:104211355-104211920	K562	blood:	n/a	n/a
47	RAD21	chr9:104211334-104212279	SK-N-SH	brain:	n/a	chr9:104211506-104211520 chr9:104211808-104211817
48	CTCF	chr9:104211740-104211890	GM12874	blood:	n/a	chr9:104211786-104211802
49	MAX	chr9:104211345-104212055	ECC-1	luminal epithelium:	n/a	n/a
50	POLR2A	chr9:104211421-104211950	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:104160996..104162683-chr9:104210087..104212007,2	K562	blood:
2	chr9:104160683..104161236-chr9:104211196..104212187,2	MCF-7	breast:
3	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]
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]
rs71491792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104210800-104212000	Active TSS	Hela-S3	cervix
2	chr9:104211000-104212000	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr9:104211000-104212000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr9:104211000-104212000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr9:104211000-104212000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr9:104211000-104212000	Enhancers	Fetal Heart	heart
7	chr9:104211000-104212200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:104211000-104212200	Active TSS	A549	lung
9	chr9:104211200-104212000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr9:104211200-104212000	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr9:104211200-104212200	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr9:104211400-104212000	Active TSS	H1 Cell Line	embryonic stem cell
13	chr9:104211400-104212000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:104211400-104212000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:104211400-104212000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:104211400-104212000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:104211400-104212000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:104211400-104212000	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr9:104211400-104212000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:104211400-104212000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr9:104211400-104212000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
22	chr9:104211400-104212000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
23	chr9:104211400-104212000	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
24	chr9:104211400-104212000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr9:104211400-104212000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr9:104211400-104212000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr9:104211400-104212000	Active TSS	Aorta	Aorta
28	chr9:104211400-104212000	Flanking Active TSS	Colonic Mucosa	Colon
29	chr9:104211400-104212000	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr9:104211400-104212000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
31	chr9:104211400-104212000	Bivalent Enhancer	Fetal Brain Male	brain
32	chr9:104211400-104212000	Active TSS	Fetal Intestine Large	intestine
33	chr9:104211400-104212000	Active TSS	Fetal Intestine Small	intestine
34	chr9:104211400-104212000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
35	chr9:104211400-104212000	Enhancers	Placenta	Placenta
36	chr9:104211400-104212000	Active TSS	Gastric	stomach
37	chr9:104211400-104212000	Active TSS	Left Ventricle	heart
38	chr9:104211400-104212000	Active TSS	Right Ventricle	heart
39	chr9:104211400-104212000	Bivalent/Poised TSS	HSMM	muscle
40	chr9:104211400-104212000	Bivalent/Poised TSS	HSMMtube	muscle
41	chr9:104211400-104212000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
42	chr9:104211400-104212000	Active TSS	NH-A	brain
43	chr9:104211400-104212000	Active TSS	NHDF-Ad	bronchial
44	chr9:104211400-104212000	Bivalent/Poised TSS	NHLF	lung
45	chr9:104211400-104212200	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr9:104211400-104212200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr9:104211400-104212200	Active TSS	Colon Smooth Muscle	Colon
48	chr9:104211600-104212000	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr9:104211600-104212000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr9:104211600-104212000	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood

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