Variant report

Variant	rs13340720
Chromosome Location	chr9:102688260-102688261
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	SETDB1	chr9:102687818-102688645	U2OS	brain:	n/a	n/a
2	KAP1	chr9:102687496-102688678	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:102685655..102688610-chr9:102689840..102691723,2	MCF-7	breast:
2	chr9:102687179..102688964-chr9:102696441..102698384,2	K562	blood:

Variant related genes	Relation type
STX17	TF binding region
ENSG00000136874	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10429611	0.81[YRI][hapmap]
rs12346672	1.00[YRI][hapmap]
rs55801872	1.00[AMR][1000 genomes]
rs55827103	1.00[AMR][1000 genomes]
rs56153123	1.00[AMR][1000 genomes]
rs73505752	1.00[AMR][1000 genomes]
rs7861003	0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	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
3	nsv831668	chr9:102568169-102747293	Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS 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	32 gene(s)	inside rSNPs	diseases
4	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
5	nsv1050510	chr9:102684318-102748658	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102669800-102729800	Weak transcription	Small Intestine	intestine
2	chr9:102670400-102688600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr9:102671200-102719200	Weak transcription	Fetal Heart	heart
4	chr9:102680000-102710800	Weak transcription	HUVEC	blood vessel
5	chr9:102680400-102693800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr9:102680400-102724800	Weak transcription	HSMM	muscle
7	chr9:102680600-102689000	Weak transcription	Fetal Brain Male	brain
8	chr9:102681800-102690400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:102682600-102693800	Weak transcription	Osteobl	bone
10	chr9:102682600-102751400	Weak transcription	NH-A	brain
11	chr9:102682800-102695000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr9:102684200-102689400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:102684400-102691400	Weak transcription	NHDF-Ad	bronchial
14	chr9:102684400-102720600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr9:102684600-102693600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr9:102684800-102689800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:102685000-102690800	Weak transcription	HSMMtube	muscle
18	chr9:102685000-102698200	Weak transcription	NHEK	skin
19	chr9:102685000-102710000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr9:102685000-102731600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr9:102685200-102730200	Weak transcription	NHLF	lung
22	chr9:102685400-102690800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr9:102685800-102689400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr9:102685800-102691000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:102685800-102698000	Weak transcription	HMEC	breast
26	chr9:102686000-102688800	Weak transcription	Left Ventricle	heart
27	chr9:102686000-102695400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr9:102686000-102699400	Weak transcription	K562	blood
29	chr9:102686200-102690800	Weak transcription	Brain Angular Gyrus	brain
30	chr9:102686200-102694400	Weak transcription	Brain Substantia Nigra	brain
31	chr9:102686200-102699200	Weak transcription	Fetal Kidney	kidney
32	chr9:102686200-102699400	Weak transcription	Psoas Muscle	Psoas
33	chr9:102686200-102730000	Weak transcription	Colonic Mucosa	Colon
34	chr9:102686400-102689000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr9:102686400-102689200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr9:102686400-102689200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr9:102686400-102693600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr9:102686400-102694600	Weak transcription	Brain Hippocampus Middle	brain
39	chr9:102686400-102694600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr9:102686400-102699400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr9:102686400-102712800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr9:102686400-102713000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr9:102686400-102723400	Weak transcription	Colon Smooth Muscle	Colon
44	chr9:102686400-102750800	Weak transcription	Esophagus	oesophagus
45	chr9:102686600-102688600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr9:102686600-102688600	Weak transcription	Fetal Lung	lung
47	chr9:102686600-102688600	Weak transcription	Spleen	Spleen
48	chr9:102686600-102688800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr9:102686600-102688800	Weak transcription	Fetal Stomach	stomach
50	chr9:102686600-102688800	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links