Variant report

Variant	rs10819764
Chromosome Location	chr9:103115528-103115529
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	HDAC2	chr9:103114906-103115583	HepG2	liver:	n/a	n/a
2	TAF1	chr9:103114966-103115550	PFSK-1	brain:	n/a	n/a
3	MAX	chr9:103114579-103115695	Hela-S3	cervix:	n/a	chr9:103115231-103115241 chr9:103115246-103115257 chr9:103115247-103115256 chr9:103115248-103115257 chr9:103115306-103115316
4	MXI1	chr9:103112680-103116753	SK-N-SH	brain:	n/a	n/a
5	EP300	chr9:103114985-103115589	HepG2	liver:	n/a	n/a
6	POLR2A	chr9:103114966-103115590	GM12878	blood:	n/a	n/a
7	POLR2A	chr9:103114784-103115566	H1-neurons	neurons:	n/a	n/a
8	POLR2A	chr9:103114939-103115588	U87	brain:	n/a	n/a
9	E2F6	chr9:103114968-103115552	A549	lung:	n/a	chr9:103115284-103115295
10	MAX	chr9:103114583-103115676	H1-hESC	embryonic stem cell:	n/a	chr9:103115231-103115241 chr9:103115246-103115257 chr9:103115247-103115256 chr9:103115248-103115257 chr9:103115306-103115316
11	POLR2A	chr9:103114919-103115632	PANC-1	pancreas:	n/a	n/a
12	HEY1	chr9:103114822-103115670	HepG2	liver:	n/a	chr9:103115062-103115077
13	SP1	chr9:103115022-103115542	GM12878	blood:	n/a	chr9:103115225-103115235 chr9:103115224-103115236 chr9:103115305-103115317 chr9:103115306-103115316 chr9:103115307-103115316 chr9:103115224-103115236 chr9:103115306-103115315 chr9:103115305-103115317 chr9:103115225-103115239 chr9:103115282-103115293 chr9:103115226-103115235 chr9:103115225-103115234 chr9:103115305-103115316 chr9:103115306-103115316 chr9:103115279-103115293
14	POLR2A	chr9:103114922-103115555	K562	blood:	n/a	n/a
15	KAP1	chr9:103114772-103115895	HEK293	kidney:	n/a	n/a
16	POLR2A	chr9:103114492-103115592	GM18505	blood:	n/a	n/a
17	POLR2A	chr9:103114527-103115549	ECC-1	luminal epithelium:	n/a	n/a
18	MAZ	chr9:103114475-103115685	Hela-S3	cervix:	n/a	chr9:103115231-103115241 chr9:103115246-103115257 chr9:103115247-103115256 chr9:103115248-103115257 chr9:103115306-103115316
19	MXI1	chr9:103114181-103115780	IMR90	lung:	n/a	n/a
20	JUN	chr9:103115051-103115544	K562	blood:	n/a	chr9:103115282-103115291
21	MAX	chr9:103114778-103115586	K562	blood:	n/a	chr9:103115231-103115241 chr9:103115246-103115257 chr9:103115247-103115256 chr9:103115248-103115257 chr9:103115306-103115316
22	E2F6	chr9:103114898-103115606	H1-hESC	embryonic stem cell:	n/a	chr9:103115284-103115295
23	MAX	chr9:103114449-103115640	NB4	blood:	n/a	chr9:103115231-103115241 chr9:103115246-103115257 chr9:103115247-103115256 chr9:103115248-103115257 chr9:103115306-103115316
24	GTF2B	chr9:103115139-103115553	K562	blood:	n/a	n/a
25	RCOR1	chr9:103114573-103115572	Hela-S3	cervix:	n/a	n/a
26	MYC	chr9:103114091-103115824	A549	lung:	n/a	chr9:103115231-103115241 chr9:103115246-103115257 chr9:103115247-103115256 chr9:103115248-103115257 chr9:103115306-103115316
27	BHLHE40	chr9:103114434-103115754	GM12878	blood:	n/a	chr9:103115280-103115296 chr9:103115241-103115262 chr9:103115063-103115079 chr9:103115245-103115258 chr9:103115246-103115255
28	TAF1	chr9:103114107-103115708	H1-hESC	embryonic stem cell:	n/a	n/a
29	USF2	chr9:103114487-103115561	GM12878	blood:	n/a	chr9:103115280-103115296 chr9:103115241-103115262 chr9:103115063-103115079 chr9:103115246-103115257 chr9:103115245-103115258 chr9:103115246-103115255
30	ELK1	chr9:103115107-103115551	K562	blood:	n/a	n/a
31	YY1	chr9:103115023-103115557	SK-N-SH_RA	brain:	n/a	chr9:103115064-103115078 chr9:103115261-103115272 chr9:103115068-103115079
32	CEBPD	chr9:103114906-103115535	HepG2	liver:	n/a	n/a
33	POLR2A	chr9:103114902-103115598	H1-neurons	neurons:	n/a	n/a
34	GTF2F1	chr9:103115077-103115615	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr9:103114808-103115664	U87	brain:	n/a	n/a
36	MYBL2	chr9:103114902-103115705	HepG2	liver:	n/a	n/a
37	POLR2A	chr9:103114207-103115599	Hela-S3	cervix:	n/a	n/a
38	TBP	chr9:103114557-103115583	H1-hESC	embryonic stem cell:	n/a	n/a
39	RUNX3	chr9:103114904-103115691	GM12878	blood:	n/a	n/a
40	TRIM28	chr9:103114896-103115757	K562	blood:	n/a	n/a
41	ZNF263	chr9:103114111-103115761	HEK293-T-REx	kidney:	n/a	n/a
42	POLR2A	chr9:103114532-103115716	GM15510	blood:	n/a	n/a
43	POLR2A	chr9:103114876-103115612	GM12891	blood:	n/a	n/a
44	POLR2A	chr9:103114913-103115581	GM10847	blood:	n/a	n/a
45	GABPA	chr9:103114962-103115529	HL-60	blood:	n/a	chr9:103115307-103115316
46	POLR2A	chr9:103114761-103115559	K562	blood:	n/a	n/a
47	GATA2	chr9:103114550-103116157	SH-SY5Y	brain:	n/a	n/a
48	KAP1	chr9:103115051-103115704	U2OS	brain:	n/a	n/a
49	REST	chr9:103115082-103115546	ECC-1	luminal epithelium:	n/a	chr9:103115225-103115238
50	POLR2A	chr9:103114788-103115605	Gliobla	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:30948635..30949371-chr9:103115049..103115906,2	HCT-116	colon:
2	chr9:103108889..103112022-chr9:103112659..103116565,8	MCF-7	breast:
3	chr9:103113352..103115792-chr9:103234740..103236804,2	K562	blood:
4	chr9:103112743..103119519-chr9:103186928..103191502,9	MCF-7	breast:
5	chr9:103112020..103116853-chr9:103187928..103193300,12	MCF-7	breast:
6	chr9:103113279..103116752-chr9:103187119..103190910,6	K562	blood:
7	chr19:18284325..18285153-chr9:103115057..103115842,2	HCT-116	colon:
8	chr9:103112440..103115986-chr9:103202100..103206037,4	K562	blood:
9	chr9:103113956..103115729-chr9:103202379..103204489,2	K562	blood:
10	chr9:103113751..103117482-chr9:103187755..103190910,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf30-1	chr9:103115261-103115863	NONHSAT133714

Variant related genes	Relation type
TEX10	TF binding region
ENSG00000241697	Chromatin interaction
ENSG00000251349	Chromatin interaction
ENSG00000066697	Chromatin interaction
ENSG00000235884	Chromatin interaction
ENSG00000136891	Chromatin interaction
ENSG00000216490	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10117799	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10118398	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10118701	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10120244	0.98[ASN][1000 genomes]
rs10123866	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10123913	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10124133	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124893	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10125785	0.88[ASN][1000 genomes]
rs10760724	0.85[ASN][1000 genomes]
rs10819751	0.85[ASN][1000 genomes]
rs10819759	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10819761	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10819762	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819767	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989049	0.88[ASN][1000 genomes]
rs10989056	0.92[ASN][1000 genomes]
rs10989064	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989067	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989070	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11789196	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12684939	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1338123	0.85[ASN][1000 genomes]
rs1338124	0.85[ASN][1000 genomes]
rs1338125	0.85[ASN][1000 genomes]
rs1930243	0.98[ASN][1000 genomes]
rs1930244	0.90[ASN][1000 genomes]
rs1961367	0.98[ASN][1000 genomes]
rs2026999	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2151131	0.90[ASN][1000 genomes]
rs2210498	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245216	0.83[ASN][1000 genomes]
rs2417084	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2417176	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485745	0.82[ASN][1000 genomes]
rs2787368	0.87[ASN][1000 genomes]
rs2787369	0.87[ASN][1000 genomes]
rs2787371	0.85[ASN][1000 genomes]
rs2787372	0.87[ASN][1000 genomes]
rs2787373	0.87[ASN][1000 genomes]
rs2787375	0.87[ASN][1000 genomes]
rs2787377	0.88[ASN][1000 genomes]
rs2787380	0.83[ASN][1000 genomes]
rs2787381	0.83[ASN][1000 genomes]
rs2787383	0.85[ASN][1000 genomes]
rs2787385	0.83[ASN][1000 genomes]
rs2787388	0.85[ASN][1000 genomes]
rs2806692	0.85[ASN][1000 genomes]
rs2806693	0.82[ASN][1000 genomes]
rs2806694	0.82[ASN][1000 genomes]
rs2806695	0.83[ASN][1000 genomes]
rs2806696	0.85[ASN][1000 genomes]
rs2806702	0.88[ASN][1000 genomes]
rs2806703	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs28464821	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3813712	0.88[ASN][1000 genomes]
rs3923501	0.88[ASN][1000 genomes]
rs4128230	0.92[ASN][1000 genomes]
rs4237195	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4237196	0.98[ASN][1000 genomes]
rs4446782	0.88[ASN][1000 genomes]
rs4742782	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4742783	0.95[ASN][1000 genomes]
rs4742784	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743392	0.88[ASN][1000 genomes]
rs4743393	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4743394	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743396	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5029342	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5029343	0.88[ASN][1000 genomes]
rs59242794	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6479008	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6479009	0.88[ASN][1000 genomes]
rs6479013	0.83[ASN][1000 genomes]
rs6479014	0.98[ASN][1000 genomes]
rs7020988	0.88[ASN][1000 genomes]
rs7021310	0.98[ASN][1000 genomes]
rs7025891	0.97[ASN][1000 genomes]
rs7025938	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7035619	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7036570	0.98[ASN][1000 genomes]
rs7047694	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7048601	0.84[ASN][1000 genomes]
rs7472	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7849966	0.88[ASN][1000 genomes]
rs7852189	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7854693	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7860513	0.98[ASN][1000 genomes]
rs7864494	0.87[ASN][1000 genomes]
rs7866850	0.98[ASN][1000 genomes]
rs7869985	0.98[ASN][1000 genomes]
rs7871702	0.98[ASN][1000 genomes]
rs7874710	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7874900	0.98[ASN][1000 genomes]
rs7875775	0.98[ASN][1000 genomes]
rs914711	0.98[ASN][1000 genomes]
rs9299338	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs944710	0.98[ASN][1000 genomes]
rs946054	0.83[ASN][1000 genomes]
rs959893	0.95[ASN][1000 genomes]
rs9775014	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9775182	0.88[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	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10819764	TEX10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103112200-103115800	Active TSS	GM12878-XiMat	blood
2	chr9:103112400-103116000	Active TSS	H9 Cell Line	embryonic stem cell
3	chr9:103112600-103116000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr9:103112800-103116000	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr9:103112800-103116000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr9:103113200-103116000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:103113200-103116000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr9:103113400-103115600	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr9:103113400-103115600	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr9:103113400-103115600	Active TSS	A549	lung
11	chr9:103113400-103115600	Active TSS	NHLF	lung
12	chr9:103113400-103116000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr9:103113400-103116000	Active TSS	NHDF-Ad	bronchial
14	chr9:103113400-103116400	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr9:103113400-103116800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:103113600-103115600	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr9:103113600-103115600	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr9:103113600-103115600	Active TSS	K562	blood
19	chr9:103113600-103115800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr9:103113600-103116000	Active TSS	H1 Cell Line	embryonic stem cell
21	chr9:103113600-103116000	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr9:103113600-103116200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:103113600-103116400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:103113800-103115800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr9:103113800-103115800	Active TSS	Primary T cells fromperipheralblood	blood
26	chr9:103113800-103115800	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr9:103113800-103115800	Active TSS	Colonic Mucosa	Colon
28	chr9:103113800-103115800	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr9:103113800-103115800	Active TSS	Psoas Muscle	Psoas
30	chr9:103113800-103115800	Active TSS	Right Atrium	heart
31	chr9:103113800-103115800	Active TSS	HSMMtube	muscle
32	chr9:103113800-103116000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:103113800-103116000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr9:103113800-103116000	Active TSS	Right Ventricle	heart
35	chr9:103113800-103116200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr9:103114000-103115600	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr9:103114000-103115600	Active TSS	Brain Anterior Caudate	brain
38	chr9:103114000-103115600	Active TSS	Brain Substantia Nigra	brain
39	chr9:103114000-103115600	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr9:103114000-103115600	Active TSS	Rectal Mucosa Donor 31	rectum
41	chr9:103114000-103115600	Active TSS	Stomach Mucosa	stomach
42	chr9:103114000-103115600	Active TSS	HSMM	muscle
43	chr9:103114000-103115800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr9:103114000-103115800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr9:103114000-103115800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr9:103114000-103115800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr9:103114000-103115800	Active TSS	Fetal Kidney	kidney
48	chr9:103114000-103115800	Active TSS	Placenta	Placenta
49	chr9:103114000-103115800	Active TSS	Ovary	ovary
50	chr9:103114000-103115800	Active TSS	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links