Variant report

Variant	rs9609264
Chromosome Location	chr22:31746719-31746720
allele	C/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	REST	chr22:31746506-31746901	ECC-1	luminal epithelium:	n/a	n/a
2	ARID3A	chr22:31746414-31746945	HepG2	liver:	n/a	n/a
3	POLR2A	chr22:31746680-31746726	ProgFib	skin:	n/a	n/a
4	MXI1	chr22:31746462-31746868	HepG2	liver:	n/a	chr22:31746624-31746639 chr22:31746626-31746641
5	REST	chr22:31746469-31746791	H1-hESC	embryonic stem cell:	n/a	n/a
6	RCOR1	chr22:31746462-31746816	K562	blood:	n/a	n/a
7	RFX5	chr22:31746466-31746798	HepG2	liver:	n/a	chr22:31746625-31746640 chr22:31746622-31746637 chr22:31746625-31746640 chr22:31746623-31746637 chr22:31746625-31746640 chr22:31746624-31746632 chr22:31746624-31746641 chr22:31746626-31746635
8	POLR2A	chr22:31746389-31746745	ECC-1	luminal epithelium:	n/a	n/a
9	SIN3A	chr22:31746478-31746828	H1-hESC	embryonic stem cell:	n/a	n/a
10	EP300	chr22:31746328-31746831	HepG2	liver:	n/a	n/a
11	MAX	chr22:31746462-31746754	H1-hESC	embryonic stem cell:	n/a	chr22:31746630-31746639 chr22:31746626-31746635
12	HDAC2	chr22:31746475-31746825	HepG2	liver:	n/a	chr22:31746493-31746507
13	POLR2A	chr22:31746488-31746942	SK-N-SH	brain:	n/a	n/a
14	MYBL2	chr22:31746403-31747017	HepG2	liver:	n/a	n/a
15	SIN3AK20	chr22:31746481-31746763	H1-hESC	embryonic stem cell:	n/a	n/a
16	REST	chr22:31746506-31746819	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr22:31746454-31746992	MCF-7	breast:	n/a	n/a
18	NFIC	chr22:31746353-31746958	ECC-1	luminal epithelium:	n/a	chr22:31746652-31746668 chr22:31746652-31746669
19	RCOR1	chr22:31746452-31746952	HepG2	liver:	n/a	n/a
20	EP300	chr22:31746433-31746813	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31738670..31747056-chr22:31790500..31799012,36	MCF-7	breast:
2	chr17:61043432..61045215-chr22:31745449..31748247,2	MCF-7	breast:

Variant related genes	Relation type
PATZ1	TF binding region
ENSG00000263931	Chromatin interaction
ENSG00000185721	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1034588	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1034589	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs12152166	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13054220	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13056485	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs131205	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13158	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1858821	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2040533	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2073857	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2078803	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2079431	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2106294	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2228619	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2273249	0.95[CEU][hapmap]
rs2273251	0.95[CEU][hapmap]
rs2283879	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2283881	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2413033	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2413034	0.81[EUR][1000 genomes]
rs2413035	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2413046	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2413047	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2413049	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2899164	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs34545960	0.84[EUR][1000 genomes]
rs4141404	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4299418	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4603880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820042	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4820043	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4820951	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4820955	1.00[CEU][hapmap]
rs4820962	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4820963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749224	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs5749229	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5749243	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5749265	0.85[EUR][1000 genomes]
rs5749267	0.84[EUR][1000 genomes]
rs5749268	0.84[EUR][1000 genomes]
rs5749270	0.84[EUR][1000 genomes]
rs5753500	0.80[EUR][1000 genomes]
rs5753521	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753543	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5753597	0.85[EUR][1000 genomes]
rs5753601	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs5753609	0.90[CEU][hapmap]
rs5753610	0.84[EUR][1000 genomes]
rs5753612	0.83[EUR][1000 genomes]
rs5753613	0.83[EUR][1000 genomes]
rs5753632	0.95[CEU][hapmap]
rs5753639	0.95[CEU][hapmap]
rs5994394	0.84[EUR][1000 genomes]
rs5997902	0.82[EUR][1000 genomes]
rs5997912	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5997913	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs5997933	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5997939	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5997949	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71324184	0.92[EUR][1000 genomes]
rs714909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs715510	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7285619	0.95[CEU][hapmap]
rs7287267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7293171	0.84[EUR][1000 genomes]
rs737684	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs737887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737888	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs738657	0.95[CEU][hapmap]
rs8135344	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8135347	0.82[EUR][1000 genomes]
rs8138596	0.91[EUR][1000 genomes]
rs8141150	0.84[EUR][1000 genomes]
rs9606830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606839	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs9606843	0.95[CEU][hapmap]
rs9609254	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609257	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9609265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609266	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609267	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9609268	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9609276	0.83[EUR][1000 genomes]
rs9609277	0.84[EUR][1000 genomes]
rs9621235	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[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	nsv834176	chr22:31682426-31864701	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	esv3333136	chr22:31704947-31758417	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	esv1816779	chr22:31743711-31797094	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9609264	DRG1	Cis_1M	lymphoblastoid	RTeQTL
rs9609264	SFI1	cis	Thyroid	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31744000-31762200	Weak transcription	Right Atrium	heart
2	chr22:31744200-31748400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr22:31744200-31750400	Weak transcription	Spleen	Spleen
4	chr22:31745200-31751400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr22:31745800-31747000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr22:31745800-31747400	Enhancers	HepG2	liver
7	chr22:31746200-31746800	Enhancers	A549	lung
8	chr22:31746200-31747000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr22:31746200-31747000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr22:31746200-31747000	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr22:31746200-31747000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr22:31746400-31747000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr22:31746400-31747000	Enhancers	Fetal Heart	heart
14	chr22:31746400-31747200	Enhancers	Liver	Liver
15	chr22:31746600-31746800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr22:31746600-31746800	Enhancers	Colon Smooth Muscle	Colon
17	chr22:31746600-31746800	Enhancers	Fetal Lung	lung
18	chr22:31746600-31746800	Enhancers	HSMMtube	muscle
19	chr22:31746600-31746800	Enhancers	NH-A	brain
20	chr22:31746600-31747000	Enhancers	Pancreas	Pancrea

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