Variant report

Variant	rs4535826
Chromosome Location	chr9:86556831-86556832
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86549593..86551703-chr9:86556254..86557805,2	MCF-7	breast:
2	chr9:86555752..86558711-chr9:86579434..86581068,2	K562	blood:
3	chr9:86554424..86556839-chr9:86571104..86572996,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165118	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10114889	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10115699	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10125715	0.85[ASN][1000 genomes]
rs10868068	0.80[ASN][1000 genomes]
rs10868070	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10868071	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10868076	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11140251	0.88[CHB][hapmap]
rs11140253	0.88[CHB][hapmap]
rs11140265	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs11140304	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12378956	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs12682981	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13290882	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap]
rs13296528	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1831757	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[ASN][1000 genomes]
rs1889113	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1982151	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[ASN][1000 genomes]
rs2378661	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs2576362	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2780103	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs296883	0.81[ASN][1000 genomes]
rs296887	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[ASN][1000 genomes]
rs296888	0.94[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.83[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs296889	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[ASN][1000 genomes]
rs296890	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.91[ASN][1000 genomes]
rs296892	0.82[YRI][hapmap]
rs296893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3180887	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs3818725	0.88[CHB][hapmap]
rs4147132	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147133	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4877814	0.82[YRI][hapmap]
rs6559751	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6559752	0.81[ASN][1000 genomes]
rs6559753	0.82[YRI][hapmap]
rs6559756	0.82[YRI][hapmap]
rs7020300	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7021189	0.82[YRI][hapmap]
rs7033292	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7045126	0.97[ASN][1000 genomes]
rs7047907	0.94[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap]
rs7853254	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7853377	0.81[AFR][1000 genomes]
rs7869321	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7875011	0.82[YRI][hapmap]
rs796003	0.90[ASN][1000 genomes]
rs796004	0.91[ASN][1000 genomes]
rs796007	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9410888	0.88[CHB][hapmap]
rs963459	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv469859	chr9:86398152-86587957	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv482641	chr9:86398152-86587957	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv8541	chr9:86469723-86593758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
7	esv3366490	chr9:86541369-86608868	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
8	nsv1043703	chr9:86545917-86603545	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4535826	UBQLN1	cis	cerebellum	SCAN
rs4535826	LOC440173	cis	parietal	SCAN
rs4535826	C9orf64	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86536600-86571000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:86543000-86571000	Weak transcription	Esophagus	oesophagus
3	chr9:86547200-86570200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr9:86548000-86567000	Weak transcription	GM12878-XiMat	blood
5	chr9:86549000-86570200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr9:86549600-86557000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr9:86550200-86557000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr9:86550200-86557200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr9:86550200-86559200	Weak transcription	Brain Anterior Caudate	brain
10	chr9:86550200-86570400	Weak transcription	Aorta	Aorta
11	chr9:86550400-86569200	Weak transcription	Fetal Heart	heart
12	chr9:86550400-86570400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr9:86550600-86559200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:86550600-86569000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:86550800-86558400	Weak transcription	NHLF	lung
16	chr9:86550800-86563800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:86550800-86568800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr9:86550800-86570400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr9:86551000-86559200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr9:86551000-86570400	Weak transcription	Stomach Mucosa	stomach
21	chr9:86551000-86570400	Weak transcription	NH-A	brain
22	chr9:86551600-86570000	Weak transcription	Fetal Brain Male	brain
23	chr9:86551600-86570200	Weak transcription	NHEK	skin
24	chr9:86552000-86562000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr9:86552000-86570400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr9:86552000-86570400	Weak transcription	Spleen	Spleen
27	chr9:86552200-86559200	Weak transcription	HSMM	muscle
28	chr9:86552400-86559400	Strong transcription	Fetal Brain Female	brain
29	chr9:86552400-86560200	Strong transcription	Adipose Nuclei	Adipose
30	chr9:86552600-86559800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr9:86552800-86560200	Strong transcription	HepG2	liver
32	chr9:86552800-86561800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr9:86553000-86557000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:86553000-86557400	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr9:86553000-86558800	Weak transcription	Fetal Kidney	kidney
36	chr9:86553000-86559200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr9:86553000-86561800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr9:86553000-86561800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr9:86553000-86570400	Weak transcription	Colonic Mucosa	Colon
40	chr9:86553200-86562200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:86553400-86557400	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr9:86553400-86559400	Strong transcription	Osteobl	bone
43	chr9:86553400-86562000	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr9:86553400-86563200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:86553600-86557600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr9:86553600-86557600	Strong transcription	Thymus	Thymus
47	chr9:86553600-86557800	Strong transcription	Brain Cingulate Gyrus	brain
48	chr9:86553600-86558400	Strong transcription	Primary T cells from cord blood	blood
49	chr9:86553600-86558600	Strong transcription	Brain Angular Gyrus	brain
50	chr9:86553600-86559400	Strong transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links