Variant report

Variant	rs10500835
Chromosome Location	chr11:18600322-18600323
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18599363..18605712-chr11:18606522..18612149,6	MCF-7	breast:
2	chr11:18597269..18603847-chr11:18605648..18613112,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151116	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11024669	0.86[EUR][1000 genomes]
rs11024677	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11024688	1.00[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11024693	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11024706	0.90[TSI][hapmap]
rs11024714	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11024715	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11024725	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024726	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024727	1.00[JPT][hapmap];0.90[TSI][hapmap]
rs12222154	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12289223	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12418726	0.90[TSI][hapmap]
rs12421394	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12574333	0.86[TSI][hapmap]
rs16935541	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16935559	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16935575	1.00[CEU][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1979051	0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs1983124	0.95[JPT][hapmap]
rs2279900	0.86[TSI][hapmap]
rs2279902	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2291751	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2292179	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2305166	0.90[TSI][hapmap]
rs3781640	1.00[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4436523	0.95[JPT][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs55969503	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61882886	0.87[EUR][1000 genomes]
rs61884673	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61884715	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61884716	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61884723	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61884724	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61886140	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61886141	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6416020	1.00[JPT][hapmap];0.86[TSI][hapmap]
rs7950602	0.90[TSI][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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv1042155	chr11:18435855-18697576	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv1046886	chr11:18547568-18781448	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv540956	chr11:18547568-18781448	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10500835	TSG101	cis	lymphoblastoid	seeQTL
rs10500835	NUCB2	cis	cerebellum	SCAN
rs10500835	UEVLD	cis	cerebellum	SCAN
rs10500835	LDHC	cis	parietal	SCAN
rs10500835	TSG101	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18549600-18608600	Weak transcription	Fetal Heart	heart
2	chr11:18549600-18609000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:18549600-18609000	Weak transcription	Fetal Brain Male	brain
4	chr11:18549800-18600600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr11:18552600-18601400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr11:18563200-18601200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr11:18563800-18608800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:18565200-18609400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:18566200-18601000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr11:18567400-18601000	Strong transcription	Placenta	Placenta
11	chr11:18568600-18600800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:18571800-18601200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr11:18574400-18609400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:18575000-18609200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr11:18575200-18609200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr11:18578000-18600600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr11:18578000-18608800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr11:18578000-18609000	Weak transcription	Right Ventricle	heart
19	chr11:18578200-18609000	Weak transcription	Primary T cells from cord blood	blood
20	chr11:18578400-18609000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr11:18578600-18608400	Weak transcription	Psoas Muscle	Psoas
22	chr11:18579600-18600800	Weak transcription	Colonic Mucosa	Colon
23	chr11:18580000-18608600	Weak transcription	Hela-S3	cervix
24	chr11:18580200-18608600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr11:18581000-18609000	Weak transcription	Pancreas	Pancrea
26	chr11:18582600-18600600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr11:18583000-18608200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr11:18583000-18609400	Weak transcription	Esophagus	oesophagus
29	chr11:18583200-18604600	Weak transcription	Gastric	stomach
30	chr11:18584200-18608000	Weak transcription	Small Intestine	intestine
31	chr11:18584400-18609800	Weak transcription	Spleen	Spleen
32	chr11:18585800-18608600	Weak transcription	Fetal Brain Female	brain
33	chr11:18586400-18609000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr11:18588200-18608800	Weak transcription	Fetal Kidney	kidney
35	chr11:18590200-18601200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr11:18590800-18601200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr11:18590800-18601400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr11:18591000-18601200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr11:18591000-18601200	Strong transcription	Adipose Nuclei	Adipose
40	chr11:18591200-18601200	Strong transcription	Fetal Muscle Leg	muscle
41	chr11:18591200-18601400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr11:18591400-18601200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr11:18591400-18601200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr11:18591800-18608800	Weak transcription	NHEK	skin
45	chr11:18592200-18600600	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr11:18592200-18600800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr11:18592200-18609000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr11:18592200-18609400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr11:18593000-18608200	Weak transcription	Brain Germinal Matrix	brain
50	chr11:18593200-18601200	Strong transcription	Liver	Liver

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