Variant report

Variant	rs1324935
Chromosome Location	chr9:115764076-115764077
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:115761496..115766057-chr9:115772281..115775505,7	K562	blood:
2	chr9:115752326..115754565-chr9:115761394..115764104,2	K562	blood:

Variant related genes	Relation type
ENSG00000228623	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10124395	0.93[AFR][1000 genomes]
rs10739384	0.89[AFR][1000 genomes]
rs10817422	0.81[AFR][1000 genomes]
rs10817425	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817426	0.89[AFR][1000 genomes]
rs11971	0.88[AFR][1000 genomes]
rs1324934	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1570755	0.83[AFR][1000 genomes]
rs1570756	0.82[JPT][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap]
rs1830870	0.88[AFR][1000 genomes]
rs2025545	0.89[AFR][1000 genomes]
rs2418245	0.82[JPT][hapmap];0.84[LWK][hapmap];0.81[MKK][hapmap]
rs4246894	0.81[LWK][hapmap]
rs4978531	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs4979204	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6477979	0.91[AFR][1000 genomes]
rs6477980	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7869125	0.88[AFR][1000 genomes]
rs974230	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv466490	chr9:115716155-115783589	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv615201	chr9:115716155-115783589	ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv430092	chr9:115716215-115790227	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1040477	chr9:115717108-115768769	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1052547	chr9:115717108-115787041	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1035654	chr9:115717108-115789896	ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1037684	chr9:115720902-115769814	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv540197	chr9:115720902-115769814	ZNF genes & repeats Enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv3379667	chr9:115743721-115782404	ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv615203	chr9:115745205-115775168	ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv466491	chr9:115745205-115814473	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
15	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
16	nsv1048246	chr9:115759281-115821188	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
17	nsv540198	chr9:115759281-115821188	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1324935	SNX30	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115753800-115768800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
2	chr9:115755400-115765200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
3	chr9:115759200-115764400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr9:115759200-115764400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr9:115759200-115764400	ZNF genes & repeats	Fetal Lung	lung
6	chr9:115759200-115765400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
7	chr9:115759200-115767000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:115759200-115768800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
9	chr9:115759200-115769000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
10	chr9:115759200-115773000	ZNF genes & repeats	Fetal Brain Female	brain
11	chr9:115759400-115764200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr9:115759400-115764200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:115759400-115764400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
14	chr9:115759400-115765400	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
15	chr9:115759400-115765600	ZNF genes & repeats	Brain Hippocampus Middle	brain
16	chr9:115759400-115768800	ZNF genes & repeats	Brain Anterior Caudate	brain
17	chr9:115759600-115764400	ZNF genes & repeats	Brain Cingulate Gyrus	brain
18	chr9:115759600-115765600	ZNF genes & repeats	Brain Germinal Matrix	brain
19	chr9:115759600-115765800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:115759600-115767000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
21	chr9:115759600-115767000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
22	chr9:115759800-115764600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:115760000-115764400	ZNF genes & repeats	HepG2	liver
24	chr9:115761600-115766400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr9:115762200-115764200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr9:115762200-115764200	Weak transcription	Aorta	Aorta
27	chr9:115762200-115764800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:115762200-115765000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr9:115762200-115768600	Weak transcription	Fetal Stomach	stomach
30	chr9:115762400-115764200	Weak transcription	Fetal Brain Male	brain
31	chr9:115762400-115764200	Weak transcription	Left Ventricle	heart
32	chr9:115762400-115765000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr9:115762400-115765200	Weak transcription	Ovary	ovary
34	chr9:115762400-115774000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr9:115762800-115774000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr9:115763600-115764400	ZNF genes & repeats	Brain Angular Gyrus	brain
37	chr9:115763600-115766800	ZNF genes & repeats	Brain Substantia Nigra	brain
38	chr9:115763800-115764400	ZNF genes & repeats	Fetal Kidney	kidney
39	chr9:115763800-115765400	ZNF genes & repeats	Stomach Smooth Muscle	stomach
40	chr9:115763800-115767000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum

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