Variant report

Variant	rs10758299
Chromosome Location	chr9:3526656-3526657
allele	A/C
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	MYC	chr9:3525549-3528177	K562	blood:	n/a	chr9:3526414-3526424
2	RCOR1	chr9:3525586-3527336	Hela-S3	cervix:	n/a	n/a
3	PML	chr9:3525812-3527014	GM12878	blood:	n/a	chr9:3526704-3526712
4	EP300	chr9:3525544-3526894	A549	lung:	n/a	chr9:3526436-3526443 chr9:3525592-3525601 chr9:3525595-3525604 chr9:3525596-3525605 chr9:3526411-3526420 chr9:3526662-3526671
5	ATF2	chr9:3525510-3527470	GM12878	blood:	n/a	n/a
6	NRF1	chr9:3526162-3527061	GM12878	blood:	n/a	chr9:3526662-3526671
7	ELF1	chr9:3526140-3526926	A549	lung:	n/a	chr9:3526434-3526447 chr9:3526436-3526445 chr9:3526435-3526446
8	ZNF143	chr9:3525591-3527555	GM12878	blood:	n/a	chr9:3526084-3526102 chr9:3526263-3526281 chr9:3526662-3526672
9	TAF1	chr9:3526087-3527137	GM12891	blood:	n/a	n/a
10	TAF1	chr9:3526125-3526937	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr9:3525818-3527501	HepG2	liver:	n/a	n/a
12	POLR2A	chr9:3525429-3527637	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAFK	chr9:3525796-3526944	IMR90	lung:	n/a	n/a
14	MAX	chr9:3525524-3527067	HepG2	liver:	n/a	chr9:3526414-3526424
15	CREB1	chr9:3526093-3527072	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr9:3525546-3527771	U87	brain:	n/a	n/a
17	TAF1	chr9:3525710-3527180	SK-N-SH	brain:	n/a	n/a
18	YY1	chr9:3526256-3526926	GM12892	blood:	n/a	chr9:3526556-3526570 chr9:3526662-3526676 chr9:3526694-3526702 chr9:3526693-3526703 chr9:3526665-3526674 chr9:3526693-3526715
19	YY1	chr9:3525772-3527075	K562	blood:	n/a	chr9:3526556-3526570 chr9:3526662-3526676 chr9:3526694-3526702 chr9:3526090-3526101 chr9:3526693-3526703 chr9:3526665-3526674 chr9:3526092-3526101 chr9:3526693-3526715
20	CEBPB	chr9:3526579-3526828	GM12878	blood:	n/a	n/a
21	MYC	chr9:3525837-3528078	MCF10A-Er-Src	breast:	n/a	chr9:3526414-3526424
22	EP300	chr9:3525569-3527202	ECC-1	luminal epithelium:	n/a	chr9:3526436-3526443 chr9:3525592-3525601 chr9:3525595-3525604 chr9:3525596-3525605 chr9:3526411-3526420 chr9:3526662-3526671
23	HDAC2	chr9:3525614-3527107	MCF-7	breast:	n/a	chr9:3526130-3526149
24	MYC	chr9:3525470-3527880	MCF10A-Er-Src	breast:	n/a	chr9:3526414-3526424
25	ZEB1	chr9:3526246-3527311	GM12878	blood:	n/a	n/a
26	PBX3	chr9:3525722-3526966	A549	lung:	n/a	n/a
27	RAD21	chr9:3526268-3527194	IMR90	lung:	n/a	chr9:3526634-3526647
28	MAX	chr9:3525576-3526981	HUVEC	blood vessel:	n/a	chr9:3526414-3526424
29	BACH1	chr9:3526523-3526941	K562	blood:	n/a	n/a
30	POLR2A	chr9:3525449-3528109	HepG2	liver:	n/a	n/a
31	MAX	chr9:3525249-3528209	NB4	blood:	n/a	chr9:3526414-3526424
32	TAF1	chr9:3525574-3527469	H1-neurons	neurons:	n/a	n/a
33	CHD2	chr9:3525779-3527244	Hela-S3	cervix:	n/a	chr9:3526447-3526457 chr9:3526442-3526452
34	POLR2A	chr9:3524442-3529266	GM12891	blood:	n/a	n/a
35	GABPA	chr9:3525885-3526829	HepG2	liver:	n/a	chr9:3526662-3526671
36	POLR2A	chr9:3520146-3530139	MCF10A-Er-Src	breast:	n/a	n/a
37	YY1	chr9:3526265-3526911	HepG2	liver:	n/a	chr9:3526556-3526570 chr9:3526662-3526676 chr9:3526694-3526702 chr9:3526693-3526703 chr9:3526665-3526674 chr9:3526693-3526715
38	CREB1	chr9:3525714-3527029	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr9:3525629-3528132	U87	brain:	n/a	n/a
40	YY1	chr9:3526165-3527351	SK-N-SH_RA	brain:	n/a	chr9:3526556-3526570 chr9:3526662-3526676 chr9:3526694-3526702 chr9:3526693-3526703 chr9:3526665-3526674 chr9:3526693-3526715
41	REST	chr9:3525744-3526937	HepG2	liver:	n/a	chr9:3526050-3526057 chr9:3526267-3526280 chr9:3526557-3526570
42	EGR1	chr9:3525618-3527392	HCT-116	colon:	n/a	chr9:3526007-3526021 chr9:3525988-3526001 chr9:3526620-3526634 chr9:3526415-3526425 chr9:3526006-3526019 chr9:3526665-3526675 chr9:3526332-3526345 chr9:3525958-3525972 chr9:3526657-3526667 chr9:3525989-3526003 chr9:3526084-3526094
43	POLR2A	chr9:3525546-3527156	A549	lung:	n/a	n/a
44	CEBPD	chr9:3525784-3527290	K562	blood:	n/a	n/a
45	MYBL2	chr9:3525939-3527075	HepG2	liver:	n/a	n/a
46	JUND	chr9:3526473-3526792	H1-hESC	embryonic stem cell:	n/a	n/a
47	TAF7	chr9:3525781-3527029	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr9:3525540-3527543	GM12878	blood:	n/a	n/a
49	HMGN3	chr9:3525467-3526951	K562	blood:	n/a	n/a
50	POLR2A	chr9:3525604-3527947	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:235530520..235531027-chr9:3526471..3527321,2	NB4	blood:
2	chr11:62608630..62609720-chr9:3525790..3526999,5	NB4	blood:
3	chr9:3466442..3469407-chr9:3524530..3526691,2	K562	blood:
4	chr9:3526066..3528514-chr9:4296505..4298964,2	MCF-7	breast:
5	chr15:63796330..63797281-chr9:3526357..3526957,2	NB4	blood:
6	chr1:228644726..228645711-chr9:3526113..3526668,2	Hela-S3	cervix:
7	chr2:25015551..25016258-chr9:3526024..3526911,2	NB4	blood:
8	chr9:3488422..3492745-chr9:3526119..3529756,3	K562	blood:
9	chr9:3525029..3527764-chr9:4296989..4300105,4	MCF-7	breast:
10	chr9:2841657..2846061-chr9:3525153..3529600,6	K562	blood:
11	chr9:3462529..3469298-chr9:3525044..3529022,8	MCF-7	breast:
12	chr2:47403392..47404127-chr9:3526386..3527170,2	NB4	blood:
13	chr7:105029252..105029910-chr9:3525726..3526715,2	NB4	blood:
14	chr9:2842064..2844768-chr9:3524803..3527756,2	K562	blood:
15	chr1:150336446..150337429-chr9:3526474..3527304,2	HCT-116	colon:
16	chr17:48943311..48943858-chr9:3525945..3526823,2	HCT-116	colon:
17	chr9:3526287..3529194-chr9:3646038..3648964,2	K562	blood:
18	chr2:55275968..55276663-chr9:3526373..3527286,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNV2-3	chr9:3526119-3532720	NONHSAT130021

Variant related genes	Relation type
ENSG00000232104	TF binding region
RFX3	TF binding region
ENSG00000116957	Chromatin interaction
ENSG00000135250	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000080608	Chromatin interaction
ENSG00000141232	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000140455	Chromatin interaction
ENSG00000228322	Chromatin interaction
ENSG00000184924	Chromatin interaction
ENSG00000138092	Chromatin interaction
ENSG00000107249	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000080298	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000203286	Chromatin interaction
ENSG00000237359	Chromatin interaction
ENSG00000181218	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10115088	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10118702	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10814189	0.83[EUR][1000 genomes]
rs10814208	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10814219	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10814233	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10814235	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10814250	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10814251	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10972435	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10972438	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1133463	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1133467	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12004862	0.87[EUR][1000 genomes]
rs12684702	0.80[ASN][1000 genomes]
rs2027089	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28510559	0.90[EUR][1000 genomes]
rs3954945	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7022948	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7027862	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7041399	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7042747	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7045092	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7847562	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7858486	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7864107	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7867083	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7871777	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7873538	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9774864	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9792451	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[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	nsv531566	chr9:3288211-3545454	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv1022795	chr9:3436845-3744623	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv539944	chr9:3476471-3535344	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10758299	RP11-509J21.1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3521800-3529000	Active TSS	GM12878-XiMat	blood
2	chr9:3522600-3530200	Active TSS	K562	blood
3	chr9:3522800-3527400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:3523000-3526800	Active TSS	NH-A	brain
5	chr9:3523000-3527200	Active TSS	Brain Anterior Caudate	brain
6	chr9:3523200-3527000	Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr9:3523200-3527200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:3523200-3527200	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr9:3523600-3528200	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr9:3523600-3528600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:3523800-3526800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:3523800-3527000	Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr9:3523800-3527000	Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr9:3524000-3527000	Active TSS	NHLF	lung
15	chr9:3524000-3527200	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr9:3524000-3527200	Active TSS	HMEC	breast
17	chr9:3524000-3527400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr9:3524000-3527400	Active TSS	NHDF-Ad	bronchial
19	chr9:3524200-3527000	Active TSS	Primary T cells fromperipheralblood	blood
20	chr9:3524200-3527000	Active TSS	Duodenum Mucosa	Duodenum
21	chr9:3524200-3527000	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr9:3524200-3527200	Active TSS	Brain Hippocampus Middle	brain
23	chr9:3524200-3527200	Active TSS	Fetal Muscle Leg	muscle
24	chr9:3524200-3527200	Active TSS	Fetal Stomach	stomach
25	chr9:3524200-3527200	Active TSS	Stomach Smooth Muscle	stomach
26	chr9:3524200-3527600	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr9:3524200-3527800	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr9:3524200-3528000	Active TSS	A549	lung
29	chr9:3524400-3526800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr9:3524400-3527000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:3524400-3527000	Active TSS	Primary B cells from peripheral blood	blood
32	chr9:3524400-3527000	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr9:3524400-3527000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr9:3524400-3527000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:3524400-3527000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr9:3524400-3527000	Active TSS	Fetal Lung	lung
37	chr9:3524400-3527000	Active TSS	Hela-S3	cervix
38	chr9:3524400-3527000	Active TSS	Osteobl	bone
39	chr9:3524400-3527200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr9:3524400-3527200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr9:3524400-3527200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr9:3524400-3527200	Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr9:3524400-3527200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr9:3524400-3527200	Active TSS	Brain Cingulate Gyrus	brain
45	chr9:3524400-3527200	Active TSS	Brain Substantia Nigra	brain
46	chr9:3524400-3527200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr9:3524400-3527200	Active TSS	Fetal Thymus	thymus
48	chr9:3524400-3527200	Active TSS	Rectal Smooth Muscle	rectum
49	chr9:3524400-3527400	Active TSS	H1 Cell Line	embryonic stem cell
50	chr9:3524400-3527400	Active TSS	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links