Variant report

Variant	rs12005806
Chromosome Location	chr9:96720847-96720848
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 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	JUND	chr9:96720814-96721064	H1-hESC	embryonic stem cell:	n/a	n/a
4	MYC	chr9:96720666-96721854	NB4	blood:	n/a	chr9:96720728-96720738
5	MAX	chr9:96720726-96721837	NB4	blood:	n/a	chr9:96720728-96720738
6	POLR2A	chr9:96720592-96721841	NB4	blood:	n/a	n/a
7	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	chr9:96720819-96720869	SK-N-SH_RA	brain:	n/a
2	chr9:96720819-96720869	HCT-116	colon:	n/a
3	chr9:96720819-96720869	GM06990	blood:	n/a
4	chr9:96720819-96720869	HCF	heart:	n/a
5	chr9:96720819-96720869	HCM	heart:	n/a
6	chr9:96720819-96720869	AG04450	lung:	fetal
7	chr9:96720819-96720869	NH-A	brain:	n/a
8	chr9:96720819-96720869	HEK293	kidney:	embryo
9	chr9:96720819-96720869	K562	blood:	n/a
10	chr9:96720819-96720869	GM12878	blood:	n/a
11	chr9:96720819-96720869	SKMC	muscle:	n/a
12	chr9:96720819-96720869	HMEC	breast:	n/a
13	chr9:96720819-96720869	GM12892	blood:	n/a
14	chr9:96720819-96720869	HAEpiC	amniotic membrane:	n/a
15	chr9:96720819-96720869	RPTEC	kidney:	n/a
16	chr9:96720819-96720869	IMR90	lung:	fetal
17	chr9:96720819-96720869	CMK	blood:	n/a
18	chr9:96720819-96720869	HRE	kidney:	n/a
19	chr9:96720819-96720869	NT2-D1	testis:	n/a
20	chr9:96720819-96720869	PrEC	prostate:	n/a
21	chr9:96720819-96720869	AG09309	skin:	n/a
22	chr9:96720819-96720869	PANC-1	pancreas:	n/a
23	chr9:96720819-96720869	HRCEpiC	kidney:	n/a
24	chr9:96720819-96720869	HL-60	blood:	n/a
25	chr9:96720819-96720869	SAEC	small airway:	n/a
26	chr9:96720819-96720869	Hepatocyte	liver:	n/a
27	chr9:96720819-96720869	MCF-7	breast:	n/a
28	chr9:96720819-96720869	GM12891	blood:	n/a
29	chr9:96720819-96720869	PFSK-1	brain:	n/a
30	chr9:96720819-96720869	HRPEpiC	eye:	n/a
31	chr9:96720819-96720869	HIPEpiC	eye:	n/a
32	chr9:96720819-96720869	SK-N-SH	brain:	n/a
33	chr9:96720819-96720869	AG10803	skin:	n/a
34	chr9:96720819-96720869	SK-N-MC	brain:	n/a
35	chr9:96720819-96720869	LNCaP	prostate:	n/a
36	chr9:96720819-96720869	HUVEC	blood vessel:	n/a
37	chr9:96720819-96720869	NB4	blood:	n/a
38	chr9:96720819-96720869	NHDF-neo	bronchial:	n/a
39	chr9:96720819-96720869	AoSMC	blood vessel:	n/a
40	chr9:96720819-96720869	BE2_C	brain:	n/a
41	chr9:96720819-96720869	ProgFib	skin:	n/a
42	chr9:96720819-96720869	HEEpiC	esophagus:	n/a
43	chr9:96720819-96720869	ECC-1	luminal epithelium:	n/a
44	chr9:96720819-96720869	ovcar-3	ovarian:	n/a
45	chr9:96720819-96720869	NHBE	bronchial:	n/a
46	chr9:96720819-96720869	Hela-S3	cervix:	n/a
47	chr9:96720819-96720869	GM19239	blood:	n/a
48	chr9:96720819-96720869	AG09319	gingival:	n/a
49	chr9:96720819-96720869	A549	lung:	n/a
50	chr9:96720819-96720869	AG04449	skin:	fetal

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:96709646..96715968-chr9:96715980..96721050,10	MCF-7	breast:
2	chr9:96718522..96721455-chr9:96725392..96727968,2	MCF-7	breast:
3	chr9:96442742..96446259-chr9:96719078..96722660,3	MCF-7	breast:
4	chr9:96720222..96721910-chr9:96722308..96724040,2	MCF-7	breast:

No data

Variant related genes	Relation type
BARX1	TF binding region
BARX1	CpG island
ENSG00000131668	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1057713	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10821273	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10821274	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11788035	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11999521	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11999551	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1320546	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13283836	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13291289	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1933680	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1933681	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1933682	0.86[AMR][1000 genomes]
rs2095778	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35001304	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4437716	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4563951	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56285369	0.80[AMR][1000 genomes]
rs7034685	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7872123	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[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:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96718400-96721000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:96718400-96721200	Weak transcription	Pancreas	Pancrea
3	chr9:96718400-96722000	Weak transcription	Hela-S3	cervix
4	chr9:96719200-96722000	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr9:96719400-96721200	Weak transcription	Gastric	stomach
6	chr9:96720200-96721000	Bivalent Enhancer	Stomach Mucosa	stomach
7	chr9:96720200-96721200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
8	chr9:96720400-96721000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr9:96720400-96721000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
10	chr9:96720400-96721000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
11	chr9:96720400-96721000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr9:96720400-96721000	Bivalent Enhancer	Fetal Muscle Leg	muscle
13	chr9:96720400-96721000	Bivalent/Poised TSS	Fetal Stomach	stomach
14	chr9:96720400-96721200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
15	chr9:96720400-96721600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr9:96720400-96723200	Bivalent Enhancer	Placenta	Placenta
17	chr9:96720400-96724400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
18	chr9:96720600-96721000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:96720600-96721000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr9:96720600-96721000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
21	chr9:96720600-96721000	Bivalent Enhancer	Primary B cells from cord blood	blood
22	chr9:96720600-96721000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr9:96720600-96721000	Bivalent Enhancer	Adipose Nuclei	Adipose
24	chr9:96720600-96721000	Bivalent Enhancer	Fetal Lung	lung
25	chr9:96720600-96721200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
26	chr9:96720600-96721200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:96720600-96721200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
28	chr9:96720600-96721200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
29	chr9:96720600-96721200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
30	chr9:96720600-96721200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
31	chr9:96720600-96721200	Bivalent Enhancer	Lung	lung
32	chr9:96720600-96721400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
33	chr9:96720600-96721400	Bivalent Enhancer	Brain Germinal Matrix	brain
34	chr9:96720600-96721400	Bivalent/Poised TSS	HepG2	liver
35	chr9:96720600-96721600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr9:96720600-96721600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
37	chr9:96720600-96721600	Bivalent Enhancer	Fetal Intestine Small	intestine
38	chr9:96720600-96721600	Active TSS	Osteobl	bone
39	chr9:96720600-96721800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
40	chr9:96720600-96721800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr9:96720600-96722000	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
42	chr9:96720600-96722000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr9:96720600-96722000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
44	chr9:96720600-96722000	Bivalent Enhancer	Fetal Brain Male	brain
45	chr9:96720600-96723200	Bivalent Enhancer	Fetal Intestine Large	intestine
46	chr9:96720600-96723400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
47	chr9:96720600-96723600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
48	chr9:96720800-96721000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
49	chr9:96720800-96721000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
50	chr9:96720800-96721000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links