Variant report

Variant	rs62574323
Chromosome Location	chr9:96721512-96721513
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SUZ12	chr9:96719499-96722002	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTBP2	chr9:96720002-96722078	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr9:96720863-96722645	H1-neurons	neurons:	n/a	n/a
4	MYC	chr9:96720666-96721854	NB4	blood:	n/a	chr9:96720728-96720738
5	EBF1	chr9:96721507-96721798	GM12878	blood:	n/a	chr9:96721664-96721673 chr9:96721664-96721673 chr9:96721664-96721674 chr9:96721663-96721674 chr9:96721662-96721675
6	SPI1	chr9:96721458-96721975	HL-60	blood:	n/a	n/a
7	POLR2A	chr9:96720912-96723257	H1-neurons	neurons:	n/a	n/a
8	MAX	chr9:96720726-96721837	NB4	blood:	n/a	chr9:96720728-96720738
9	POLR2A	chr9:96720592-96721841	NB4	blood:	n/a	n/a
10	GABPA	chr9:96721085-96721592	H1-hESC	embryonic stem cell:	n/a	n/a
11	SUZ12	chr9:96720177-96723275	NT2-D1	testis:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:96721468-96721518	HUVEC	blood vessel:	n/a
2	chr9:96721468-96721518	LNCaP	prostate:	n/a
3	chr9:96721468-96721518	GM12878	blood:	n/a
4	chr9:96721468-96721518	MCF10A-Er-Src	breast:	n/a
5	chr9:96721468-96721518	HRCEpiC	kidney:	n/a
6	chr9:96721468-96721518	SK-N-SH_RA	brain:	n/a
7	chr9:96721468-96721518	NH-A	brain:	n/a
8	chr9:96721468-96721518	H1-hESC	embryonic stem cell:	embryo
9	chr9:96721468-96721518	NHDF-neo	bronchial:	n/a
10	chr9:96721468-96721518	GM12892	blood:	n/a
11	chr9:96721468-96721518	HRE	kidney:	n/a
12	chr9:96721468-96721518	HIPEpiC	eye:	n/a
13	chr9:96721468-96721518	Hepatocyte	liver:	n/a
14	chr9:96721468-96721518	MCF-7	breast:	n/a
15	chr9:96721468-96721518	K562	blood:	n/a
16	chr9:96721468-96721518	AG10803	skin:	n/a
17	chr9:96721468-96721518	HAEpiC	amniotic membrane:	n/a
18	chr9:96721468-96721518	IMR90	lung:	fetal
19	chr9:96721468-96721518	HCM	heart:	n/a
20	chr9:96721468-96721518	PANC-1	pancreas:	n/a
21	chr9:96721468-96721518	NT2-D1	testis:	n/a
22	chr9:96721468-96721518	RPTEC	kidney:	n/a
23	chr9:96721468-96721518	AoSMC	blood vessel:	n/a
24	chr9:96721468-96721518	AG09319	gingival:	n/a
25	chr9:96721468-96721518	HL-60	blood:	n/a
26	chr9:96721468-96721518	SAEC	small airway:	n/a
27	chr9:96721468-96721518	SKMC	muscle:	n/a
28	chr9:96721468-96721518	T-47D	breast:	n/a
29	chr9:96721468-96721518	NB4	blood:	n/a
30	chr9:96721468-96721518	Caco-2	colon:	n/a
31	chr9:96721468-96721518	Hela-S3	cervix:	n/a
32	chr9:96721468-96721518	GM12891	blood:	n/a
33	chr9:96721468-96721518	HRPEpiC	eye:	n/a
34	chr9:96721468-96721518	ovcar-3	ovarian:	n/a
35	chr9:96721468-96721518	NHBE	bronchial:	n/a
36	chr9:96721468-96721518	HCT-116	colon:	n/a
37	chr9:96721468-96721518	CMK	blood:	n/a
38	chr9:96721468-96721518	ECC-1	luminal epithelium:	n/a
39	chr9:96721468-96721518	BE2_C	brain:	n/a
40	chr9:96721468-96721518	HEEpiC	esophagus:	n/a
41	chr9:96721468-96721518	HMEC	breast:	n/a
42	chr9:96721468-96721518	Jurkat	blood:	n/a
43	chr9:96721468-96721518	SK-N-MC	brain:	n/a
44	chr9:96721468-96721518	HPAEpiC	pulmonary alveolar:	n/a
45	chr9:96721468-96721518	HEK293	kidney:	embryo
46	chr9:96721468-96721518	HNPCEpiC	eye:	n/a
47	chr9:96721468-96721518	AG09309	skin:	n/a
48	chr9:96721468-96721518	HCF	heart:	n/a
49	chr9:96721468-96721518	ProgFib	skin:	n/a
50	chr9:96721468-96721518	PrEC	prostate:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:96442742..96446259-chr9:96719078..96722660,3	MCF-7	breast:
2	chr9:96720222..96721910-chr9:96722308..96724040,2	MCF-7	breast:

No data

Variant related genes	Relation type
BARX1	TF binding region
BARX1	CpG island

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10993017	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11788160	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11789015	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11792744	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11793856	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12001386	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12684081	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1411861	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2095777	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2153791	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2398893	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34849895	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35001304	0.87[AFR][1000 genomes]
rs35480828	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35886839	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4316201	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5014099	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55947603	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56285369	0.84[EUR][1000 genomes]
rs56335449	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62574346	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7849645	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7858520	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[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	nsv893589	chr9:96624645-96884544	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv824993	chr9:96699362-96725105	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893590	chr9:96701287-96729129	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96718400-96722000	Weak transcription	Hela-S3	cervix
2	chr9:96719200-96722000	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr9:96720400-96721600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr9:96720400-96723200	Bivalent Enhancer	Placenta	Placenta
5	chr9:96720400-96724400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr9:96720600-96721600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:96720600-96721600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
8	chr9:96720600-96721600	Bivalent Enhancer	Fetal Intestine Small	intestine
9	chr9:96720600-96721600	Active TSS	Osteobl	bone
10	chr9:96720600-96721800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr9:96720600-96721800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr9:96720600-96722000	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
13	chr9:96720600-96722000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:96720600-96722000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
15	chr9:96720600-96722000	Bivalent Enhancer	Fetal Brain Male	brain
16	chr9:96720600-96723200	Bivalent Enhancer	Fetal Intestine Large	intestine
17	chr9:96720600-96723400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
18	chr9:96720600-96723600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
19	chr9:96720800-96721600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
20	chr9:96720800-96721600	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr9:96720800-96721600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:96720800-96721600	Bivalent Enhancer	Left Ventricle	heart
23	chr9:96720800-96721800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:96720800-96721800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr9:96720800-96721800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr9:96720800-96722000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
27	chr9:96720800-96722000	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
28	chr9:96720800-96722000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
29	chr9:96720800-96723200	Bivalent Enhancer	Spleen	Spleen
30	chr9:96721000-96721600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:96721000-96721600	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr9:96721000-96721600	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
33	chr9:96721000-96721600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
34	chr9:96721000-96721600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
35	chr9:96721000-96721600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
36	chr9:96721000-96721600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
37	chr9:96721000-96721600	Flanking Active TSS	Right Atrium	heart
38	chr9:96721000-96721600	Bivalent Enhancer	Small Intestine	intestine
39	chr9:96721000-96721600	Flanking Bivalent TSS/Enh	NHEK	skin
40	chr9:96721000-96721800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr9:96721000-96721800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
42	chr9:96721000-96721800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:96721000-96721800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
44	chr9:96721000-96721800	Bivalent Enhancer	Psoas Muscle	Psoas
45	chr9:96721000-96722000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
46	chr9:96721000-96722000	Bivalent Enhancer	Fetal Heart	heart
47	chr9:96721000-96722000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
48	chr9:96721200-96721600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr9:96721200-96721600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
50	chr9:96721200-96721600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood

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