Variant report

Variant	rs3808896
Chromosome Location	chr9:101472177-101472178
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	RAD21	chr9:101471813-101472203	H1-hESC	embryonic stem cell:	n/a	chr9:101472046-101472060 chr9:101472042-101472061
2	REST	chr9:101471019-101472181	ECC-1	luminal epithelium:	n/a	chr9:101471384-101471394 chr9:101471411-101471424
3	REST	chr9:101471971-101473236	K562	blood:	n/a	chr9:101472860-101472869 chr9:101472855-101472864 chr9:101472849-101472869 chr9:101472373-101472391 chr9:101472849-101472869 chr9:101472931-101472944 chr9:101472856-101472869
4	RAD21	chr9:101471607-101472293	H1-hESC	embryonic stem cell:	n/a	chr9:101472046-101472060 chr9:101472042-101472061 chr9:101471608-101471622
5	RAD21	chr9:101471855-101472204	H1-hESC	embryonic stem cell:	n/a	chr9:101472046-101472060 chr9:101472042-101472061
6	CTCF	chr9:101471893-101472229	H1-hESC	embryonic stem cell:	n/a	chr9:101472044-101472062 chr9:101472046-101472059 chr9:101472039-101472060 chr9:101471978-101471991
7	CTCF	chr9:101472040-101472190	GM12873	blood:	n/a	chr9:101472044-101472062 chr9:101472046-101472059
8	CTCF	chr9:101471880-101472275	K562	blood:	n/a	chr9:101472044-101472062 chr9:101472046-101472059 chr9:101472039-101472060 chr9:101471978-101471991
9	TEAD4	chr9:101471966-101472208	H1-hESC	embryonic stem cell:	n/a	n/a
10	ZNF143	chr9:101471990-101472184	H1-hESC	embryonic stem cell:	n/a	chr9:101472042-101472060
11	CTCF	chr9:101472040-101472190	HPAF	blood vessel:	n/a	chr9:101472044-101472062 chr9:101472046-101472059
12	REST	chr9:101471070-101473423	HL-60	blood:	n/a	chr9:101471384-101471394 chr9:101472860-101472869 chr9:101472855-101472864 chr9:101471411-101471424 chr9:101472849-101472869 chr9:101472373-101472391 chr9:101472849-101472869 chr9:101472931-101472944 chr9:101472856-101472869
13	ZNF263	chr9:101471138-101473084	HEK293-T-REx	kidney:	n/a	n/a
14	REST	chr9:101472099-101473321	A549	lung:	n/a	chr9:101472860-101472869 chr9:101472855-101472864 chr9:101472849-101472869 chr9:101472373-101472391 chr9:101472849-101472869 chr9:101472931-101472944 chr9:101472856-101472869

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:101472149-101472199	SAEC	small airway:	n/a
2	chr9:101472149-101472199	AoSMC	blood vessel:	n/a
3	chr9:101472149-101472199	HRCEpiC	kidney:	n/a
4	chr9:101472149-101472199	NHDF-neo	bronchial:	n/a
5	chr9:101472149-101472199	H1-hESC	embryonic stem cell:	embryo
6	chr9:101472149-101472199	GM12878	blood:	n/a
7	chr9:101472149-101472199	HCF	heart:	n/a
8	chr9:101472149-101472199	MCF10A-Er-Src	breast:	n/a
9	chr9:101472149-101472199	HCT-116	colon:	n/a
10	chr9:101472149-101472199	AG04450	lung:	fetal
11	chr9:101472149-101472199	PrEC	prostate:	n/a
12	chr9:101472149-101472199	BE2_C	brain:	n/a
13	chr9:101472149-101472199	NB4	blood:	n/a
14	chr9:101472149-101472199	ECC-1	luminal epithelium:	n/a
15	chr9:101472149-101472199	Jurkat	blood:	n/a
16	chr9:101472149-101472199	AG09309	skin:	n/a
17	chr9:101472149-101472199	SK-N-SH	brain:	n/a
18	chr9:101472149-101472199	RPTEC	kidney:	n/a
19	chr9:101472149-101472199	NHBE	bronchial:	n/a
20	chr9:101472149-101472199	Caco-2	colon:	n/a
21	chr9:101472149-101472199	ProgFib	skin:	n/a
22	chr9:101472149-101472199	HIPEpiC	eye:	n/a
23	chr9:101472149-101472199	PFSK-1	brain:	n/a
24	chr9:101472149-101472199	U87	brain:	n/a
25	chr9:101472149-101472199	HCPEpiC	choroid plexus:	n/a
26	chr9:101472149-101472199	AG04449	skin:	fetal
27	chr9:101472149-101472199	HRE	kidney:	n/a
28	chr9:101472149-101472199	GM12891	blood:	n/a
29	chr9:101472149-101472199	Hela-S3	cervix:	n/a
30	chr9:101472149-101472199	CMK	blood:	n/a
31	chr9:101472149-101472199	HepG2	liver:	n/a
32	chr9:101472149-101472199	GM12892	blood:	n/a
33	chr9:101472149-101472199	AG10803	skin:	n/a
34	chr9:101472149-101472199	NH-A	brain:	n/a
35	chr9:101472149-101472199	LNCaP	prostate:	n/a
36	chr9:101472149-101472199	HEK293	kidney:	embryo
37	chr9:101472149-101472199	NT2-D1	testis:	n/a
38	chr9:101472149-101472199	SK-N-MC	brain:	n/a
39	chr9:101472149-101472199	HMEC	breast:	n/a
40	chr9:101472149-101472199	GM06990	blood:	n/a
41	chr9:101472149-101472199	HCM	heart:	n/a
42	chr9:101472149-101472199	HUVEC	blood vessel:	n/a
43	chr9:101472149-101472199	IMR90	lung:	fetal
44	chr9:101472149-101472199	HPAEpiC	pulmonary alveolar:	n/a
45	chr9:101472149-101472199	GM19239	blood:	n/a
46	chr9:101472149-101472199	K562	blood:	n/a
47	chr9:101472149-101472199	PANC-1	pancreas:	n/a
48	chr9:101472149-101472199	ovcar-3	ovarian:	n/a
49	chr9:101472149-101472199	HRPEpiC	eye:	n/a
50	chr9:101472149-101472199	HAEpiC	amniotic membrane:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:101390132..101392094-chr9:101471584..101473721,2	MCF-7	breast:
2	chr9:101242548..101244258-chr9:101471901..101474101,2	MCF-7	breast:

Variant related genes	Relation type
GABBR2	TF binding region
GABBR2	CpG island

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10512258	0.82[CEU][hapmap]
rs1571927	0.83[EUR][1000 genomes]
rs186808	1.00[CEU][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1930139	0.87[MEX][hapmap];0.83[EUR][1000 genomes]
rs2225558	0.83[EUR][1000 genomes]
rs337526	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs337528	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs337529	0.82[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs337532	0.82[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs337533	1.00[CEU][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs337534	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs337537	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs337538	0.85[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs337539	0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs337540	0.91[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs337541	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs337542	0.91[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs337543	0.91[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs337544	1.00[CEU][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs337545	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs337546	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs337547	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs337548	0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs337549	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs337550	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs337551	1.00[CEU][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs337552	1.00[CEU][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs337553	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs337554	0.83[JPT][hapmap]
rs337556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337557	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs337558	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs337559	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs337560	0.91[CHB][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs337561	0.84[ASN][1000 genomes]
rs394488	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs405430	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs415902	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743248	0.83[EUR][1000 genomes]
rs4743263	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs4743265	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs507876	1.00[ASN][1000 genomes]
rs509747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs526590	0.90[ASN][1000 genomes]
rs529269	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs529278	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs570138	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6478811	0.82[CEU][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv893614	chr9:101340316-101671634	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv893615	chr9:101356515-101678036	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv893616	chr9:101371017-101472921	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv825007	chr9:101467848-101476292	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv3338088	chr9:101469131-101473529	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv819653	chr9:101469511-101472192	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv3498543	chr9:101469881-101473129	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv3498544	chr9:101469881-101473129	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv3423249	chr9:101470556-101473104	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3808896	ANKS6	Cis_1M	lymphoblastoid	RTeQTL
rs3808896	SEC61B	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101469200-101472200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr9:101470000-101472200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr9:101470800-101472200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
4	chr9:101470800-101472400	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:101471200-101472200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr9:101471400-101472200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:101471400-101472200	Bivalent Enhancer	Spleen	Spleen
8	chr9:101471600-101472200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:101471600-101472200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:101471600-101472200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
11	chr9:101471600-101472200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr9:101471600-101472200	Bivalent Enhancer	Placenta	Placenta
13	chr9:101471600-101472400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr9:101471600-101472800	Enhancers	Gastric	stomach
15	chr9:101471800-101472200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr9:101471800-101472200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:101471800-101472200	Bivalent Enhancer	Liver	Liver
18	chr9:101471800-101472200	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
19	chr9:101471800-101472200	Bivalent Enhancer	Fetal Muscle Leg	muscle
20	chr9:101471800-101472200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
21	chr9:101472000-101472200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
22	chr9:101472000-101472200	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr9:101472000-101472200	Bivalent/Poised TSS	Brain Angular Gyrus	brain
24	chr9:101472000-101472200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
25	chr9:101472000-101472200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
26	chr9:101472000-101472200	Bivalent Enhancer	Small Intestine	intestine
27	chr9:101472000-101472200	Bivalent Enhancer	Stomach Smooth Muscle	stomach
28	chr9:101472000-101472400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
29	chr9:101472000-101472400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:101472000-101472400	Bivalent Enhancer	Fetal Intestine Large	intestine
31	chr9:101472000-101472800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
32	chr9:101472000-101472800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
33	chr9:101472000-101474000	Weak transcription	Right Atrium	heart

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