Variant report

Variant	rs59397123
Chromosome Location	chr9:96714338-96714339
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:122)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SUZ12	chr9:96709708-96717433	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTBP2	chr9:96710652-96717425	H1-hESC	embryonic stem cell:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:96714295-96714345	HRCEpiC	kidney:	n/a
2	chr9:96714313-96714363	HEK293	kidney:	embryo
3	chr9:96714313-96714363	SK-N-SH_RA	brain:	n/a
4	chr9:96714313-96714363	HCM	heart:	n/a
5	chr9:96714313-96714363	ovcar-3	ovarian:	n/a
6	chr9:96714295-96714345	GM12892	blood:	n/a
7	chr9:96714313-96714363	BE2_C	brain:	n/a
8	chr9:96714313-96714363	SK-N-SH	brain:	n/a
9	chr9:96714313-96714363	ECC-1	luminal epithelium:	n/a
10	chr9:96714313-96714363	HRE	kidney:	n/a
11	chr9:96714295-96714345	HCT-116	colon:	n/a
12	chr9:96714295-96714345	NH-A	brain:	n/a
13	chr9:96714295-96714345	AG04449	skin:	fetal
14	chr9:96714295-96714345	AG04450	lung:	fetal
15	chr9:96714313-96714363	MCF10A-Er-Src	breast:	n/a
16	chr9:96714295-96714345	ovcar-3	ovarian:	n/a
17	chr9:96714313-96714363	HEEpiC	esophagus:	n/a
18	chr9:96714295-96714345	SKMC	muscle:	n/a
19	chr9:96714295-96714345	HRE	kidney:	n/a
20	chr9:96714313-96714363	SKMC	muscle:	n/a
21	chr9:96714313-96714363	K562	blood:	n/a
22	chr9:96714313-96714363	AG10803	skin:	n/a
23	chr9:96714295-96714345	HCF	heart:	n/a
24	chr9:96714295-96714345	RPTEC	kidney:	n/a
25	chr9:96714313-96714363	HL-60	blood:	n/a
26	chr9:96714313-96714363	NHDF-neo	bronchial:	n/a
27	chr9:96714313-96714363	HCT-116	colon:	n/a
28	chr9:96714313-96714363	LNCaP	prostate:	n/a
29	chr9:96714313-96714363	T-47D	breast:	n/a
30	chr9:96714313-96714363	RPTEC	kidney:	n/a
31	chr9:96714295-96714345	HRPEpiC	eye:	n/a
32	chr9:96714313-96714363	HNPCEpiC	eye:	n/a
33	chr9:96714295-96714345	PFSK-1	brain:	n/a
34	chr9:96714313-96714363	HMEC	breast:	n/a
35	chr9:96714313-96714363	Hepatocyte	liver:	n/a
36	chr9:96714313-96714363	A549	lung:	n/a
37	chr9:96714313-96714363	BJ	skin:	n/a
38	chr9:96714295-96714345	PrEC	prostate:	n/a
39	chr9:96714295-96714345	SK-N-SH_RA	brain:	n/a
40	chr9:96714313-96714363	HCPEpiC	choroid plexus:	n/a
41	chr9:96714295-96714345	GM12891	blood:	n/a
42	chr9:96714295-96714345	NB4	blood:	n/a
43	chr9:96714313-96714363	AG09319	gingival:	n/a
44	chr9:96714313-96714363	ProgFib	skin:	n/a
45	chr9:96714295-96714345	BJ	skin:	n/a
46	chr9:96714313-96714363	GM06990	blood:	n/a
47	chr9:96714295-96714345	MCF-7	breast:	n/a
48	chr9:96714313-96714363	GM12892	blood:	n/a
49	chr9:96714295-96714345	HCPEpiC	choroid plexus:	n/a
50	chr9:96714295-96714345	SK-N-MC	brain:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr9:96706258..96707958-chr9:96711820..96714339,2	MCF-7	breast:
2	chr9:96713619..96716485-chr9:96717370..96719166,2	K562	blood:
3	chr9:96710465..96712948-chr9:96713592..96715312,2	MCF-7	breast:
4	chr9:96709646..96715968-chr9:96715980..96721050,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000235601	TF binding region
ENSG00000235601	CpG island
ENSG00000235601	Chromatin interaction
ENSG00000131668	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1057715	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10821275	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10821279	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992998	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10992999	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10993002	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10993004	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993005	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993006	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993007	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10993012	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10993013	0.94[EUR][1000 genomes]
rs10993015	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10993016	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10993019	0.89[ASN][1000 genomes]
rs10993029	0.89[ASN][1000 genomes]
rs12156437	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12375599	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1316935	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16909605	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16909652	0.89[ASN][1000 genomes]
rs1933683	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4269597	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4330748	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57693373	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72755516	0.83[EUR][1000 genomes]
rs72755517	0.83[EUR][1000 genomes]
rs73519466	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96711600-96715600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
2	chr9:96712800-96714800	Bivalent/Poised TSS	HSMM	muscle
3	chr9:96713000-96714400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
4	chr9:96713000-96714400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
5	chr9:96713000-96714600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
6	chr9:96713000-96714800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr9:96713000-96715800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
8	chr9:96713000-96717000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
9	chr9:96713200-96714400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
10	chr9:96713200-96714600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr9:96713200-96714600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr9:96713200-96715000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:96713200-96715000	Bivalent Enhancer	Fetal Heart	heart
14	chr9:96713200-96716400	Bivalent Enhancer	Fetal Brain Male	brain
15	chr9:96713400-96714600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr9:96713400-96714800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
17	chr9:96713600-96714600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
18	chr9:96713600-96716400	Weak transcription	Hela-S3	cervix
19	chr9:96713800-96714400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
20	chr9:96713800-96714400	Bivalent Enhancer	Primary B cells from cord blood	blood
21	chr9:96713800-96714400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
22	chr9:96713800-96714400	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
23	chr9:96713800-96714600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
24	chr9:96713800-96714600	Bivalent Enhancer	Stomach Mucosa	stomach
25	chr9:96713800-96715000	Bivalent Enhancer	Fetal Intestine Small	intestine
26	chr9:96713800-96715200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr9:96713800-96715200	Bivalent Enhancer	Fetal Intestine Large	intestine
28	chr9:96713800-96715200	Bivalent Enhancer	Placenta	Placenta
29	chr9:96713800-96715800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr9:96713800-96715800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
31	chr9:96713800-96716000	Bivalent Enhancer	Fetal Lung	lung
32	chr9:96713800-96716400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
33	chr9:96713800-96716600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
34	chr9:96713800-96716800	Bivalent Enhancer	Brain Germinal Matrix	brain
35	chr9:96713800-96716800	Bivalent Enhancer	Brain Substantia Nigra	brain
36	chr9:96713800-96717000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr9:96713800-96717200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
38	chr9:96713800-96717400	Bivalent Enhancer	Fetal Muscle Leg	muscle
39	chr9:96713800-96717800	Bivalent Enhancer	Liver	Liver
40	chr9:96713800-96718400	Bivalent Enhancer	Lung	lung
41	chr9:96714000-96714400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
42	chr9:96714000-96714400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr9:96714000-96714400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
44	chr9:96714000-96714400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
45	chr9:96714000-96714400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr9:96714000-96714400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
47	chr9:96714000-96714400	Flanking Active TSS	Ovary	ovary
48	chr9:96714000-96714600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
49	chr9:96714000-96714600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
50	chr9:96714000-96714600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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