Variant report

Variant	rs10965321
Chromosome Location	chr9:2241091-2241092
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	chr9:2240721..2243292-chr9:2621569..2623384,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236404	Chromatin interaction
ENSG00000147852	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10117698	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10118415	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10965323	0.88[GIH][hapmap]
rs1408334	0.81[AMR][1000 genomes]
rs4741658	0.86[CHB][hapmap];0.90[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016148	chr9:1457605-2361750	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv539916	chr9:1457605-2361750	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv892057	chr9:2144687-2241994	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv892059	chr9:2198627-2255397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1033628	chr9:2215179-2303623	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv539927	chr9:2215179-2303623	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv892060	chr9:2218129-2261944	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv466078	chr9:2218129-2621030	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv613126	chr9:2218129-2621030	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv6457	chr9:2228493-2271756	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv892061	chr9:2229694-2262889	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv1029947	chr9:2233969-2364269	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv1015332	chr9:2235123-2361722	Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv1022726	chr9:2235500-2361890	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv539928	chr9:2235500-2361890	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv1033537	chr9:2235700-2361750	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv539929	chr9:2235700-2361750	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv613127	chr9:2237390-2363874	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10965321	RANBP6	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2230000-2241200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:2230200-2241200	Weak transcription	Stomach Mucosa	stomach
3	chr9:2235000-2241200	Weak transcription	HMEC	breast
4	chr9:2235200-2241200	Weak transcription	NHEK	skin
5	chr9:2235200-2241400	Weak transcription	Right Ventricle	heart
6	chr9:2235400-2241200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr9:2235400-2241400	Weak transcription	Esophagus	oesophagus
8	chr9:2235400-2241400	Weak transcription	Psoas Muscle	Psoas
9	chr9:2235600-2241400	Weak transcription	Colon Smooth Muscle	Colon
10	chr9:2235800-2241200	Weak transcription	Fetal Heart	heart
11	chr9:2236000-2241400	Weak transcription	Left Ventricle	heart
12	chr9:2237600-2241200	Weak transcription	Fetal Kidney	kidney
13	chr9:2238000-2242000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr9:2239400-2241400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr9:2240200-2241800	Weak transcription	HepG2	liver
16	chr9:2240400-2241200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:2240400-2241400	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr9:2240400-2241400	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr9:2240400-2242400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr9:2240600-2241200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr9:2240800-2241200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:2240800-2241400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr9:2240800-2241600	Enhancers	Fetal Brain Male	brain
24	chr9:2241000-2241200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr9:2241000-2241200	Enhancers	H1 Cell Line	embryonic stem cell
26	chr9:2241000-2241200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:2241000-2241200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:2241000-2241200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:2241000-2241200	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr9:2241000-2241200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr9:2241000-2241200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr9:2241000-2241200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr9:2241000-2241200	Enhancers	Adipose Nuclei	Adipose
34	chr9:2241000-2241200	Active TSS	Brain Cingulate Gyrus	brain
35	chr9:2241000-2241200	Flanking Active TSS	Brain Germinal Matrix	brain
36	chr9:2241000-2241200	Enhancers	Brain Substantia Nigra	brain
37	chr9:2241000-2241200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr9:2241000-2241200	Enhancers	Fetal Lung	lung
39	chr9:2241000-2241200	Enhancers	Fetal Muscle Leg	muscle
40	chr9:2241000-2241200	Enhancers	Fetal Stomach	stomach
41	chr9:2241000-2241200	Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr9:2241000-2241200	Enhancers	HUVEC	blood vessel
43	chr9:2241000-2241200	Enhancers	NH-A	brain
44	chr9:2241000-2241400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr9:2241000-2241400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr9:2241000-2241400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr9:2241000-2241600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr9:2241000-2241600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr9:2241000-2241600	Flanking Active TSS	Fetal Brain Female	brain
50	chr9:2241000-2241800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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