Variant report

Variant	rs10817440
Chromosome Location	chr9:115874994-115874995
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	FOS	chr9:115874849-115875225	MCF10A-Er-Src	breast:	n/a	chr9:115875035-115875044 chr9:115875036-115875045 chr9:115875035-115875045
2	CTCF	chr9:115874791-115875279	HCT-116	colon:	n/a	n/a
3	MYC	chr9:115874867-115875206	MCF10A-Er-Src	breast:	n/a	n/a
4	NFIC	chr9:115874918-115875276	ECC-1	luminal epithelium:	n/a	chr9:115875047-115875063
5	RAD21	chr9:115874972-115875257	HepG2	liver:	n/a	chr9:115875086-115875095
6	STAT3	chr9:115874866-115875231	MCF10A-Er-Src	breast:	n/a	n/a
7	JUND	chr9:115874904-115875255	HepG2	liver:	n/a	chr9:115875034-115875045 chr9:115875035-115875044 chr9:115875036-115875045 chr9:115875035-115875045
8	CTCF	chr9:115874930-115875246	HepG2	liver:	n/a	n/a
9	CTCF	chr9:115873846-115875286	SK-N-SH	brain:	n/a	n/a
10	STAT3	chr9:115874861-115875230	MCF10A-Er-Src	breast:	n/a	n/a
11	CTCF	chr9:115874927-115875632	K562	blood:	n/a	chr9:115875291-115875309 chr9:115875292-115875308 chr9:115875294-115875307 chr9:115875294-115875307
12	CTCF	chr9:115874891-115874997	HUVEC	blood vessel:	n/a	n/a
13	FOS	chr9:115874862-115875231	MCF10A-Er-Src	breast:	n/a	chr9:115875035-115875044 chr9:115875036-115875045 chr9:115875035-115875045
14	CTCF	chr9:115874947-115875266	MCF-7	breast:	n/a	n/a
15	RAD21	chr9:115874943-115875261	H1-hESC	embryonic stem cell:	n/a	chr9:115875086-115875095
16	CTCF	chr9:115874980-115875259	T-47D	breast:	n/a	n/a
17	RAD21	chr9:115874969-115875280	MCF-7	breast:	n/a	chr9:115875086-115875095
18	CTCF	chr9:115874946-115875570	A549	lung:	n/a	chr9:115875291-115875309 chr9:115875292-115875308 chr9:115875294-115875307 chr9:115875294-115875307
19	STAT3	chr9:115874924-115875217	MCF10A-Er-Src	breast:	n/a	n/a
20	CTCF	chr9:115874745-115875282	HCT-116	colon:	n/a	n/a
21	CTCF	chr9:115874987-115875530	A549	lung:	n/a	chr9:115875291-115875309 chr9:115875292-115875308 chr9:115875294-115875307 chr9:115875294-115875307
22	CTCF	chr9:115874852-115875269	MCF-7	breast:	n/a	n/a
23	STAT3	chr9:115874839-115875291	MCF10A-Er-Src	breast:	n/a	n/a
24	CTCF	chr9:115874890-115875350	GM12878	blood:	n/a	chr9:115875291-115875309 chr9:115875292-115875308 chr9:115875294-115875307 chr9:115875294-115875307
25	FOS	chr9:115874862-115875252	MCF10A-Er-Src	breast:	n/a	chr9:115875035-115875044 chr9:115875036-115875045 chr9:115875035-115875045
26	RAD21	chr9:115874881-115875286	SK-N-SH	brain:	n/a	chr9:115875086-115875095
27	CTCF	chr9:115874963-115875243	H1-hESC	embryonic stem cell:	n/a	n/a
28	FOS	chr9:115874749-115875225	MCF10A-Er-Src	breast:	n/a	chr9:115875035-115875044 chr9:115875036-115875045 chr9:115875035-115875045
29	CTCF	chr9:115874814-115875290	A549	lung:	n/a	n/a
30	CTCF	chr9:115874917-115875879	K562	blood:	n/a	chr9:115875291-115875309 chr9:115875292-115875308 chr9:115875294-115875307 chr9:115875294-115875307
31	RAD21	chr9:115874884-115875278	HCT-116	colon:	n/a	chr9:115875086-115875095
32	CTCF	chr9:115874987-115875803	K562	blood:	n/a	chr9:115875291-115875309 chr9:115875292-115875308 chr9:115875294-115875307 chr9:115875294-115875307
33	MYC	chr9:115874940-115875187	MCF10A-Er-Src	breast:	n/a	n/a
34	CTCF	chr9:115874790-115875350	K562	blood:	n/a	chr9:115875291-115875309 chr9:115875292-115875308 chr9:115875294-115875307 chr9:115875294-115875307

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:115872624..115875532-chr9:115912017..115913734,2	MCF-7	breast:

Variant related genes	Relation type
FAM225B	TF binding region
FAM225A	TF binding region
ENSG00000136867	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10817438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817444	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10981632	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10981633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10981638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12552080	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2009977	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs944302	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv1047000	chr9:115610445-115884038	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv831691	chr9:115754699-115929459	Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv825051	chr9:115811606-115882022	ZNF genes & repeats Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv825052	chr9:115811634-115882048	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv893734	chr9:115815398-115891009	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv2757353	chr9:115815398-115892245	ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv2753302	chr9:115819870-115888112	ZNF genes & repeats Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
11	nsv893735	chr9:115821854-115891009	ZNF genes & repeats Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv2421517	chr9:115852715-115874994	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv893736	chr9:115852715-115891009	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv893737	chr9:115852715-115893229	Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv893738	chr9:115852715-115894240	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv1046217	chr9:115854339-115881588	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv1042807	chr9:115854339-115883741	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv1040513	chr9:115854339-115885060	Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv442164	chr9:115854351-115883753	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	esv2761253	chr9:115854351-115885060	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	nsv893739	chr9:115859223-115891009	Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	nsv893740	chr9:115860251-115891009	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
23	nsv893741	chr9:115862518-115891009	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
24	nsv893742	chr9:115867276-115910991	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
25	nsv893743	chr9:115867276-115917783	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10817440	TXN	cis	parietal	SCAN
rs10817440	SLC46A2	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115874000-115875000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
2	chr9:115874000-115875000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:115874000-115875000	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr9:115874000-115875000	Enhancers	NHEK	skin
5	chr9:115874000-115875200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:115874000-115875200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr9:115874000-115875200	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr9:115874000-115875200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:115874000-115875200	Enhancers	Brain Hippocampus Middle	brain
10	chr9:115874000-115875200	Enhancers	HMEC	breast
11	chr9:115874000-115875200	Enhancers	HSMM	muscle
12	chr9:115874200-115875200	Enhancers	Adipose Nuclei	Adipose
13	chr9:115874400-115875200	Enhancers	Osteobl	bone
14	chr9:115874800-115875200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr9:115874800-115875200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr9:115874800-115875200	Enhancers	Brain Anterior Caudate	brain
17	chr9:115874800-115875200	Enhancers	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links