Variant report

Variant	rs10972359
Chromosome Location	chr9:3524877-3524878
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	MAX	chr9:3524473-3524912	NB4	blood:	n/a	chr9:3524737-3524747
2	POLR2A	chr9:3524442-3529266	GM12891	blood:	n/a	n/a
3	POLR2A	chr9:3520146-3530139	MCF10A-Er-Src	breast:	n/a	n/a
4	WRNIP1	chr9:3524590-3525339	GM12878	blood:	n/a	n/a
5	RCOR1	chr9:3524465-3524923	GM12878	blood:	n/a	n/a
6	NFIC	chr9:3524432-3525017	GM12878	blood:	n/a	n/a
7	JUND	chr9:3524583-3524897	K562	blood:	n/a	n/a
8	ATF2	chr9:3524505-3525038	GM12878	blood:	n/a	n/a
9	POLR2A	chr9:3524528-3527972	Raji	blood:	n/a	n/a
10	POLR2A	chr9:3524545-3524880	GM12892	blood:	n/a	n/a
11	RELA	chr9:3524533-3527987	GM12891	blood:	n/a	n/a
12	TBP	chr9:3524544-3525133	K562	blood:	n/a	n/a
13	EP300	chr9:3524388-3524938	K562	blood:	n/a	chr9:3524456-3524470
14	MAZ	chr9:3524576-3524904	Hela-S3	cervix:	n/a	chr9:3524737-3524747
15	ZNF143	chr9:3524545-3524898	GM12878	blood:	n/a	n/a
16	FOXA2	chr9:3524611-3525010	A549	lung:	n/a	n/a
17	BHLHE40	chr9:3524430-3524925	GM12878	blood:	n/a	n/a
18	POLR2A	chr9:3524553-3524889	GM12891	blood:	n/a	n/a
19	SIN3A	chr9:3524488-3527318	GM12878	blood:	n/a	chr9:3525124-3525133
20	CHD1	chr9:3524393-3527671	IMR90	lung:	n/a	chr9:3524990-3525000 chr9:3526447-3526457 chr9:3526442-3526452
21	SIN3A	chr9:3524486-3527356	H1-hESC	embryonic stem cell:	n/a	chr9:3525124-3525133
22	IRF1	chr9:3524340-3524919	K562	blood:	n/a	chr9:3524710-3524730 chr9:3524457-3524471 chr9:3524459-3524472 chr9:3524711-3524728 chr9:3524712-3524726 chr9:3524461-3524471 chr9:3524712-3524723
23	MAZ	chr9:3524529-3527468	GM12878	blood:	n/a	chr9:3524987-3524997 chr9:3524737-3524747 chr9:3526414-3526424
24	ZNF384	chr9:3524360-3524924	GM12878	blood:	n/a	n/a
25	MAZ	chr9:3524511-3524898	HepG2	liver:	n/a	chr9:3524737-3524747
26	POLR2A	chr9:3524624-3528172	HepG2	liver:	n/a	n/a
27	BCLAF1	chr9:3524371-3524958	GM12878	blood:	n/a	chr9:3524461-3524470
28	POLR2A	chr9:3523584-3529804	MCF10A-Er-Src	breast:	n/a	n/a
29	RCOR1	chr9:3524572-3527358	K562	blood:	n/a	n/a
30	RCOR1	chr9:3524635-3524902	K562	blood:	n/a	n/a
31	FOXA2	chr9:3524518-3525050	A549	lung:	n/a	n/a
32	POLR2A	chr9:3524509-3528133	GM18526	blood:	n/a	n/a
33	MAZ	chr9:3524552-3527286	K562	blood:	n/a	chr9:3524987-3524997 chr9:3524737-3524747 chr9:3526414-3526424
34	BCLAF1	chr9:3524511-3524995	GM12878	blood:	n/a	n/a
35	POLR2A	chr9:3524489-3528155	GM19099	blood:	n/a	n/a
36	POLR2A	chr9:3524470-3529021	GM12878	blood:	n/a	n/a
37	POLR2A	chr9:3524539-3524911	GM12892	blood:	n/a	n/a
38	CHD1	chr9:3524542-3529139	GM12878	blood:	n/a	chr9:3524990-3525000 chr9:3526447-3526457 chr9:3526442-3526452
39	STAT1	chr9:3524731-3524896	GM12878	blood:	n/a	n/a
40	MAZ	chr9:3524291-3527504	IMR90	lung:	n/a	chr9:3524987-3524997 chr9:3524737-3524747 chr9:3526414-3526424
41	ETS1	chr9:3524558-3525004	GM12878	blood:	n/a	chr9:3524806-3524815 chr9:3524989-3525000 chr9:3524987-3524998
42	POLR2A	chr9:3524465-3528199	IMR90	lung:	n/a	n/a
43	MXI1	chr9:3524347-3525182	GM12878	blood:	n/a	n/a
44	POLR2A	chr9:3524559-3524970	GM12892	blood:	n/a	n/a
45	CHD2	chr9:3524587-3524901	GM12878	blood:	n/a	n/a
46	FOXA1	chr9:3524590-3524945	HepG2	liver:	n/a	n/a
47	POLR2A	chr9:3524485-3525276	K562	blood:	n/a	n/a
48	POLR2A	chr9:3524417-3524995	GM12892	blood:	n/a	n/a
49	TCF7L2	chr9:3524570-3524983	HCT-116	colon:	n/a	chr9:3524707-3524717 chr9:3524709-3524718
50	TBL1XR1	chr9:3524461-3524896	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:3501077..3503324-chr9:3523015..3525744,2	MCF-7	breast:
2	chr9:3466442..3469407-chr9:3524530..3526691,2	K562	blood:
3	chr9:3510896..3512703-chr9:3523478..3525761,2	MCF-7	breast:
4	chr9:2842064..2844768-chr9:3524803..3527756,2	K562	blood:
5	chr10:102106174..102108019-chr9:3523293..3526279,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232104	TF binding region
ENSG00000099194	Chromatin interaction
ENSG00000203286	Chromatin interaction
ENSG00000080608	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12004862	0.81[EUR][1000 genomes]
rs28510559	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	esv1421431	chr9:3524858-3524878	Active TSS Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv416759	chr9:3524859-3524878	Active TSS Flanking Active TSS Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10972359	RP11-509J21.1	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3512000-3525000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:3515600-3525000	Weak transcription	Small Intestine	intestine
3	chr9:3521800-3529000	Active TSS	GM12878-XiMat	blood
4	chr9:3522600-3530200	Active TSS	K562	blood
5	chr9:3522800-3527400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:3523000-3526800	Active TSS	NH-A	brain
7	chr9:3523000-3527200	Active TSS	Brain Anterior Caudate	brain
8	chr9:3523200-3525000	Active TSS	Brain Germinal Matrix	brain
9	chr9:3523200-3527000	Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr9:3523200-3527200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:3523200-3527200	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr9:3523600-3525400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr9:3523600-3528200	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr9:3523600-3528600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:3523800-3525000	Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr9:3523800-3526800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr9:3523800-3527000	Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr9:3523800-3527000	Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr9:3524000-3527000	Active TSS	NHLF	lung
20	chr9:3524000-3527200	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr9:3524000-3527200	Active TSS	HMEC	breast
22	chr9:3524000-3527400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:3524000-3527400	Active TSS	NHDF-Ad	bronchial
24	chr9:3524200-3525000	Flanking Active TSS	HUVEC	blood vessel
25	chr9:3524200-3525400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr9:3524200-3525600	Active TSS	Fetal Brain Male	brain
27	chr9:3524200-3526200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr9:3524200-3527000	Active TSS	Primary T cells fromperipheralblood	blood
29	chr9:3524200-3527000	Active TSS	Duodenum Mucosa	Duodenum
30	chr9:3524200-3527000	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr9:3524200-3527200	Active TSS	Brain Hippocampus Middle	brain
32	chr9:3524200-3527200	Active TSS	Fetal Muscle Leg	muscle
33	chr9:3524200-3527200	Active TSS	Fetal Stomach	stomach
34	chr9:3524200-3527200	Active TSS	Stomach Smooth Muscle	stomach
35	chr9:3524200-3527600	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr9:3524200-3527800	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr9:3524200-3528000	Active TSS	A549	lung
38	chr9:3524400-3525000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr9:3524400-3525000	Flanking Active TSS	NHEK	skin
40	chr9:3524400-3525200	Active TSS	HepG2	liver
41	chr9:3524400-3525400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
42	chr9:3524400-3525400	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr9:3524400-3526000	Active TSS	Right Atrium	heart
44	chr9:3524400-3526600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr9:3524400-3526600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr9:3524400-3526800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr9:3524400-3527000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:3524400-3527000	Active TSS	Primary B cells from peripheral blood	blood
49	chr9:3524400-3527000	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr9:3524400-3527000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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