Variant report

Variant	rs10818468
Chromosome Location	chr9:100836889-100836890
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	CTCF	chr9:100836639-100837117	IMR90	lung:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
2	SMC3	chr9:100836642-100837073	Hela-S3	cervix:	n/a	chr9:100836864-100836874 chr9:100836842-100836856
3	CTCF	chr9:100836694-100836954	SK-N-SH_RA	brain:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
4	CTCF	chr9:100836740-100836890	GM12871	blood:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
5	CTCF	chr9:100836780-100836930	MCF-7	breast:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
6	CTCF	chr9:100836740-100836890	MCF-7	breast:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
7	CTCF	chr9:100836659-100837004	GM12878	blood:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
8	CTCF	chr9:100836717-100836946	Hela-S3	cervix:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
9	CTCF	chr9:100836780-100836930	Caco-2	colon:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
10	CTCF	chr9:100836780-100836930	HUVEC	blood vessel:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
11	CTCF	chr9:100836628-100837068	GM12878	blood:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
12	WRNIP1	chr9:100836763-100837054	GM12878	blood:	n/a	n/a
13	CTCF	chr9:100836820-100836970	GM12868	blood:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
14	CTCF	chr9:100836740-100836890	GM12865	blood:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
15	CTCF	chr9:100836760-100836910	SK-N-SH_RA	brain:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
16	CTCF	chr9:100836740-100836890	HL-60	blood:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
17	CTCF	chr9:100836780-100836930	HBMEC	blood vessel:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
18	CTCF	chr9:100836780-100836930	K562	blood:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
19	CTCF	chr9:100836704-100836976	MCF-7	breast:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
20	CTCF	chr9:100836760-100836910	HFF-Myc	foreskin:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
21	CTCF	chr9:100836800-100836950	AG09309	skin:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
22	CTCF	chr9:100836780-100836930	GM12870	blood:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
23	POLR2A	chr9:100836361-100837041	Hela-S3	cervix:	n/a	n/a
24	RAD21	chr9:100836691-100837091	ECC-1	luminal epithelium:	n/a	chr9:100836841-100836860
25	CTCF	chr9:100836780-100836930	GM12864	blood:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
26	RAD21	chr9:100836666-100837073	HepG2	liver:	n/a	chr9:100836841-100836860
27	RAD21	chr9:100836696-100837053	A549	lung:	n/a	chr9:100836841-100836860
28	CTCF	chr9:100836740-100836890	HFF-Myc	foreskin:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
29	CTCF	chr9:100836740-100836890	HFF	foreskin:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
30	CTCF	chr9:100836760-100836910	HepG2	liver:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
31	YY1	chr9:100836703-100836912	GM12891	blood:	n/a	n/a
32	CTCF	chr9:100836760-100836910	GM12867	blood:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
33	CTCF	chr9:100836676-100836992	K562	blood:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
34	RAD21	chr9:100836539-100837090	SK-N-SH_RA	brain:	n/a	chr9:100836841-100836860
35	CTCF	chr9:100836687-100836970	GM10248	blood:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
36	CTCF	chr9:100836503-100837197	MCF-7	breast:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
37	YY1	chr9:100836644-100836924	GM12878	blood:	n/a	n/a
38	FOS	chr9:100836778-100836978	MCF10A-Er-Src	breast:	n/a	n/a
39	RAD21	chr9:100836652-100837071	Hela-S3	cervix:	n/a	chr9:100836841-100836860
40	CTCF	chr9:100836710-100836978	GM13976	blood:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
41	CTCF	chr9:100836780-100836930	HEEpiC	esophagus:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
42	POLR2A	chr9:100836833-100837114	GM12878	blood:	n/a	n/a
43	RUNX3	chr9:100836633-100837007	GM12878	blood:	n/a	n/a
44	CTCF	chr9:100836640-100837078	MCF-7	breast:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
45	CTCF	chr9:100836740-100836890	GM12874	blood:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
46	RAD21	chr9:100836620-100837170	H1-hESC	embryonic stem cell:	n/a	chr9:100836841-100836860
47	CTCF	chr9:100836644-100836963	GM12891	blood:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
48	CTCF	chr9:100836750-100836945	GM20000	blood:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858
49	JUND	chr9:100836623-100836993	K562	blood:	n/a	n/a
50	CTCF	chr9:100836740-100836890	GM12872	blood:	n/a	chr9:100836842-100836863 chr9:100836841-100836857 chr9:100836843-100836856 chr9:100836840-100836858

No.	Distal block	Cell Line	Cell type
1	chr9:100836616..100838130-chr9:100853751..100855728,2	K562	blood:
2	chr9:100822595..100824589-chr9:100834188..100836915,2	MCF-7	breast:
3	chr9:100745732..100748566-chr9:100835046..100837989,2	MCF-7	breast:
4	chr9:100835251..100838541-chr9:100953348..100956508,6	MCF-7	breast:
5	chr9:100744956..100747904-chr9:100835369..100837055,2	K562	blood:
6	chr9:100836599..100837275-chr9:100996445..100997215,2	MCF-7	breast:
7	chr9:100744716..100748585-chr9:100832900..100838437,10	MCF-7	breast:
8	chr9:100817775..100822653-chr9:100832609..100840095,16	MCF-7	breast:
9	chr9:100683356..100686345-chr9:100832359..100837233,6	MCF-7	breast:
10	chr9:100817802..100822153-chr9:100831375..100837110,8	MCF-7	breast:
11	chr9:100744956..100747210-chr9:100835059..100837055,2	K562	blood:

Variant related genes	Relation type
NANS	TF binding region
ENSG00000106789	Chromatin interaction
ENSG00000224001	Chromatin interaction
ENSG00000106785	Chromatin interaction
ENSG00000136932	Chromatin interaction
ENSG00000136938	Chromatin interaction
ENSG00000095380	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10124238	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1058446	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10818454	0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs10818472	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10984977	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12348197	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12349452	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12685502	0.87[CHD][hapmap];0.81[AMR][1000 genomes]
rs16912590	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28489815	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7855984	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7874696	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9969738	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9969813	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482635	chr9:100775549-100953239	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1040483	chr9:100835325-100868437	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10818468	GNRH1	trans	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100819600-100848400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:100820000-100843000	Weak transcription	Brain Substantia Nigra	brain
3	chr9:100820000-100843200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:100820000-100843200	Weak transcription	Brain Germinal Matrix	brain
5	chr9:100820000-100843200	Weak transcription	Fetal Brain Female	brain
6	chr9:100820000-100847200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr9:100820000-100849600	Weak transcription	Fetal Brain Male	brain
8	chr9:100820000-100850000	Weak transcription	Fetal Kidney	kidney
9	chr9:100820200-100843000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr9:100821200-100849600	Weak transcription	Right Atrium	heart
11	chr9:100823800-100842000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr9:100824600-100840000	Weak transcription	Ovary	ovary
13	chr9:100824800-100840000	Weak transcription	Right Ventricle	heart
14	chr9:100824800-100843200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:100827200-100841200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr9:100827400-100838400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr9:100827600-100838200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr9:100828600-100843200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr9:100828800-100837000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:100828800-100837800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr9:100828800-100843200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr9:100829000-100837000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr9:100829000-100843600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr9:100829800-100837000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr9:100829800-100840000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:100830200-100843000	Weak transcription	NH-A	brain
27	chr9:100832200-100839400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr9:100832200-100841200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr9:100833200-100838600	Enhancers	Stomach Mucosa	stomach
30	chr9:100834200-100837600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr9:100834200-100838800	Weak transcription	HSMM	muscle
32	chr9:100834400-100837800	Weak transcription	HSMMtube	muscle
33	chr9:100834600-100837000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr9:100834600-100837400	Enhancers	Fetal Intestine Large	intestine
35	chr9:100834600-100839800	Weak transcription	Lung	lung
36	chr9:100834800-100839400	Weak transcription	Fetal Stomach	stomach
37	chr9:100834800-100840000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr9:100834800-100840200	Weak transcription	Pancreas	Pancrea
39	chr9:100835400-100837000	Weak transcription	Thymus	Thymus
40	chr9:100835600-100839800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr9:100835600-100840200	Weak transcription	Esophagus	oesophagus
42	chr9:100836000-100837000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
43	chr9:100836000-100837200	Enhancers	A549	lung
44	chr9:100836000-100837400	Enhancers	HepG2	liver
45	chr9:100836000-100838600	Enhancers	Colonic Mucosa	Colon
46	chr9:100836200-100837200	Enhancers	Gastric	stomach
47	chr9:100836200-100839200	Enhancers	Primary T cells fromperipheralblood	blood
48	chr9:100836400-100837000	Enhancers	Fetal Muscle Leg	muscle
49	chr9:100836400-100837000	Enhancers	Hela-S3	cervix
50	chr9:100836400-100837200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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