Variant report

Variant	rs35566702
Chromosome Location	chr9:96067214-96067215
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	CREB1	chr9:96067130-96067420	A549	lung:	n/a	n/a
2	RAD21	chr9:96067144-96067527	Hela-S3	cervix:	n/a	chr9:96067331-96067350
3	CTCF	chr9:96067108-96067498	A549	lung:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349
4	CTCF	chr9:96067202-96067498	Fibrobl	skin:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349
5	CTCF	chr9:96067189-96067497	MCF-7	breast:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349
6	CTCF	chr9:96067206-96067448	T-47D	breast:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349
7	CTCF	chr9:96067126-96067632	MCF-7	breast:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349
8	CTCF	chr9:96067180-96067330	WI-38	lung:	n/a	n/a
9	CTCF	chr9:96067158-96067544	IMR90	lung:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349
10	SMC3	chr9:96066928-96067706	SK-N-SH	brain:	n/a	chr9:96067607-96067617 chr9:96067335-96067349
11	RAD21	chr9:96067099-96067597	HepG2	liver:	n/a	chr9:96067331-96067350
12	CTCF	chr9:96066965-96067736	HCT-116	colon:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349
13	GABPA	chr9:96067142-96067487	H1-hESC	embryonic stem cell:	n/a	n/a
14	RAD21	chr9:96067084-96067657	ECC-1	luminal epithelium:	n/a	chr9:96067331-96067350
15	CTCF	chr9:96067200-96067491	MCF-7	breast:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349
16	RFX5	chr9:96067211-96067512	HepG2	liver:	n/a	chr9:96067390-96067399 chr9:96067387-96067402 chr9:96067388-96067402 chr9:96067393-96067401
17	CTCF	chr9:96067164-96067489	ECC-1	luminal epithelium:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349
18	RCOR1	chr9:96067206-96067514	HepG2	liver:	n/a	n/a
19	SMC3	chr9:96067170-96067526	GM12878	blood:	n/a	chr9:96067335-96067349
20	CTCF	chr9:96067197-96067492	MCF-7	breast:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349
21	YY1	chr9:96067150-96067523	HepG2	liver:	n/a	n/a
22	RAD21	chr9:96067183-96067518	GM12878	blood:	n/a	chr9:96067331-96067350
23	ZNF143	chr9:96067170-96067500	H1-hESC	embryonic stem cell:	n/a	chr9:96067276-96067294
24	SMC3	chr9:96067143-96067599	HepG2	liver:	n/a	chr9:96067335-96067349
25	SMC3	chr9:96067158-96067532	K562	blood:	n/a	chr9:96067335-96067349
26	CTCF	chr9:96067180-96067330	GM12868	blood:	n/a	n/a
27	RAD21	chr9:96067134-96067539	H1-hESC	embryonic stem cell:	n/a	chr9:96067331-96067350
28	CHD2	chr9:96067184-96067316	Hela-S3	cervix:	n/a	n/a
29	CTCF	chr9:96067160-96067478	K562	blood:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349
30	RAD21	chr9:96067072-96067560	H1-hESC	embryonic stem cell:	n/a	chr9:96067331-96067350
31	CTCF	chr9:96067209-96067492	ProgFib	skin:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349
32	MAZ	chr9:96067193-96067512	K562	blood:	n/a	n/a
33	CTCF	chr9:96067204-96067473	GM12891	blood:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349
34	CTCF	chr9:96067019-96067668	SK-N-SH	brain:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349
35	CTCF	chr9:96067196-96067496	MCF-7	breast:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349
36	CTCF	chr9:96067212-96067484	K562	blood:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349
37	CTCF	chr9:96067203-96067475	SK-N-SH_RA	brain:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349
38	RAD21	chr9:96066958-96067715	HCT-116	colon:	n/a	chr9:96067331-96067350
39	RAD21	chr9:96067072-96067447	H1-hESC	embryonic stem cell:	n/a	chr9:96067331-96067350
40	CTCF	chr9:96067130-96067475	K562	blood:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349
41	RAD21	chr9:96067037-96067602	MCF-7	breast:	n/a	chr9:96067331-96067350
42	CTCF	chr9:96066624-96067745	A549	lung:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349 chr9:96066924-96066937
43	CTCF	chr9:96067213-96067479	A549	lung:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349
44	TCF12	chr9:96066940-96067524	A549	lung:	n/a	chr9:96067401-96067409
45	TCF7L2	chr9:96067137-96067608	PANC-1	pancreas:	n/a	n/a
46	CTCF	chr9:96067204-96067504	Gliobla	brain:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349
47	POLR2A	chr9:96066962-96067357	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr9:96067104-96067551	H1-hESC	embryonic stem cell:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349
49	CTCF	chr9:96067195-96067486	GM12892	blood:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349
50	CTCF	chr9:96067150-96067560	HepG2	liver:	n/a	chr9:96067339-96067348 chr9:96067333-96067351 chr9:96067335-96067348 chr9:96067334-96067350 chr9:96067328-96067349

No.	Distal block	Cell Line	Cell type
1	chr9:96062588..96064123-chr9:96065486..96067429,2	MCF-7	breast:
2	chr9:95921958..95922909-chr9:96066342..96067827,12	MCF-7	breast:
3	chr9:95921846..95923192-chr9:96065668..96067944,24	MCF-7	breast:
4	chr9:95894765..95898074-chr9:96066261..96068998,4	MCF-7	breast:
5	chr9:96066434..96068269-chr9:96211890..96214349,2	MCF-7	breast:
6	chr9:95918199..95918816-chr9:96066893..96067580,2	K562	blood:
7	chr9:95857138..95859184-chr9:96066087..96068302,2	MCF-7	breast:
8	chr9:95871178..95872022-chr9:96066905..96067658,3	MCF-7	breast:
9	chr9:95871548..95872053-chr9:96066937..96067600,2	K562	blood:
10	chr9:96065577..96067663-chr9:96072266..96075048,2	K562	blood:
11	chr9:96063114..96067393-chr9:96338286..96340131,3	MCF-7	breast:
12	chr9:96067174..96067901-chr9:96190059..96191048,3	MCF-7	breast:
13	chr9:96062175..96064911-chr9:96066749..96068321,2	K562	blood:
14	chr9:96067102..96067655-chr9:96298858..96299574,2	MCF-7	breast:
15	chr9:96039029..96039838-chr9:96066882..96068045,4	MCF-7	breast:
16	chr9:95766003..95766670-chr9:96067179..96067717,2	MCF-7	breast:
17	chr9:96026528..96027045-chr9:96066909..96067829,2	MCF-7	breast:
18	chr9:96062201..96063792-chr9:96065861..96068764,2	MCF-7	breast:

Variant related genes	Relation type
WNK2	TF binding region
ENSG00000048828	Chromatin interaction
ENSG00000197724	Chromatin interaction
ENSG00000223446	Chromatin interaction
ENSG00000188938	Chromatin interaction
ENSG00000165233	Chromatin interaction
ENSG00000131669	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10992646	1.00[ASN][1000 genomes]
rs10992647	1.00[ASN][1000 genomes]
rs10992649	1.00[ASN][1000 genomes]
rs10992650	1.00[ASN][1000 genomes]
rs10992651	1.00[ASN][1000 genomes]
rs10992654	1.00[ASN][1000 genomes]
rs10992656	1.00[ASN][1000 genomes]
rs10992657	1.00[ASN][1000 genomes]
rs10992661	1.00[ASN][1000 genomes]
rs10992699	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11789723	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12000967	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12002458	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12005950	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12006039	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13283550	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13289160	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13296817	0.80[EUR][1000 genomes]
rs1931364	1.00[ASN][1000 genomes]
rs35199621	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36081907	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744213	1.00[ASN][1000 genomes]
rs55981123	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479471	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479474	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022051	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7023262	1.00[ASN][1000 genomes]
rs7042943	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7848843	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7857220	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866300	1.00[ASN][1000 genomes]
rs7867954	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875384	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893583	chr9:95996573-96091688	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv893584	chr9:96002983-96116937	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96033400-96077200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:96033600-96072800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr9:96051400-96067800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:96055600-96080200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr9:96056400-96079800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr9:96056800-96067400	Weak transcription	Brain Anterior Caudate	brain
7	chr9:96061000-96072200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr9:96061200-96067400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr9:96061400-96075000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr9:96061600-96070200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:96061600-96079000	Weak transcription	Gastric	stomach
12	chr9:96062600-96069200	Enhancers	Fetal Muscle Leg	muscle
13	chr9:96063000-96070200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:96063200-96072200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr9:96063400-96067400	Weak transcription	Adipose Nuclei	Adipose
16	chr9:96063400-96069200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr9:96063600-96070600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr9:96063800-96067400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr9:96063800-96088600	Weak transcription	Right Atrium	heart
20	chr9:96064800-96070200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr9:96065000-96067600	Enhancers	Fetal Brain Male	brain
22	chr9:96065000-96067600	Weak transcription	Fetal Intestine Large	intestine
23	chr9:96065000-96079200	Weak transcription	Colonic Mucosa	Colon
24	chr9:96065200-96067400	Weak transcription	Stomach Mucosa	stomach
25	chr9:96065200-96080000	Weak transcription	Spleen	Spleen
26	chr9:96065400-96073200	Strong transcription	Fetal Intestine Small	intestine
27	chr9:96065600-96067400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr9:96065600-96068000	Enhancers	Brain Germinal Matrix	brain
29	chr9:96065600-96069200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr9:96065800-96067800	Enhancers	Fetal Brain Female	brain
31	chr9:96066000-96082800	Weak transcription	Fetal Thymus	thymus
32	chr9:96066200-96067400	Weak transcription	Colon Smooth Muscle	Colon
33	chr9:96066200-96068800	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr9:96066400-96067600	Enhancers	Right Ventricle	heart
35	chr9:96066600-96067800	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr9:96066600-96067800	Genic enhancers	Fetal Stomach	stomach
37	chr9:96066600-96068400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr9:96066800-96067800	Enhancers	Brain Cingulate Gyrus	brain
39	chr9:96066800-96068600	Enhancers	Left Ventricle	heart
40	chr9:96066800-96068800	Enhancers	Psoas Muscle	Psoas
41	chr9:96067000-96067400	Enhancers	HepG2	liver
42	chr9:96067000-96068400	Enhancers	H1 Cell Line	embryonic stem cell
43	chr9:96067000-96068400	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr9:96067000-96068400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr9:96067000-96068600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr9:96067000-96070000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr9:96067200-96067600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr9:96067200-96067600	Enhancers	Brain Substantia Nigra	brain
49	chr9:96067200-96068400	Enhancers	Brain Angular Gyrus	brain
50	chr9:96067200-96069000	Enhancers	Brain Hippocampus Middle	brain

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