Variant report

Variant	rs10853097
Chromosome Location	chr17:46198162-46198163
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46123246..46128677-chr17:46197755..46203630,8	MCF-7	breast:
2	chr17:46197608..46199562-chr17:46200754..46203056,2	MCF-7	breast:
3	chr17:46197348..46200242-chr17:46209628..46212447,2	MCF-7	breast:
4	chr17:46108859..46110468-chr17:46197931..46199848,2	MCF-7	breast:
5	chr17:46183753..46186040-chr17:46196094..46199275,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000002919	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000082641	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1010228	0.91[ASN][1000 genomes]
rs1010230	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11079808	0.84[ASN][1000 genomes]
rs11079809	0.91[ASN][1000 genomes]
rs12600980	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12936369	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12941295	0.84[ASN][1000 genomes]
rs12943543	0.84[ASN][1000 genomes]
rs12950213	0.80[ASN][1000 genomes]
rs12950402	0.84[ASN][1000 genomes]
rs1452662	0.81[ASN][1000 genomes]
rs1452663	0.81[ASN][1000 genomes]
rs1452665	0.81[ASN][1000 genomes]
rs16953927	0.81[ASN][1000 genomes]
rs16953941	0.81[ASN][1000 genomes]
rs1860866	0.91[ASN][1000 genomes]
rs208005	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs208008	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs208009	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs208011	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs208012	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs208019	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2109983	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2109984	0.84[ASN][1000 genomes]
rs2325784	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2325804	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2325885	0.81[ASN][1000 genomes]
rs34980108	0.81[ASN][1000 genomes]
rs35688835	0.84[ASN][1000 genomes]
rs36071506	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3744346	0.91[ASN][1000 genomes]
rs3785737	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3815472	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4794441	0.84[ASN][1000 genomes]
rs4794448	0.84[ASN][1000 genomes]
rs4794449	0.84[ASN][1000 genomes]
rs4794450	0.83[ASN][1000 genomes]
rs4794451	0.84[ASN][1000 genomes]
rs4794453	0.84[ASN][1000 genomes]
rs55696440	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62064953	0.83[ASN][1000 genomes]
rs6504031	0.84[ASN][1000 genomes]
rs6504032	0.82[ASN][1000 genomes]
rs71356520	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71356521	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7209585	0.83[ASN][1000 genomes]
rs7209730	0.91[ASN][1000 genomes]
rs7218700	0.87[ASN][1000 genomes]
rs7222136	0.91[ASN][1000 genomes]
rs7224461	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs741058	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8065670	0.84[ASN][1000 genomes]
rs8065993	0.84[ASN][1000 genomes]
rs8066049	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8066391	0.86[ASN][1000 genomes]
rs8071199	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8075500	0.82[ASN][1000 genomes]
rs8076380	0.84[ASN][1000 genomes]
rs8077860	0.84[ASN][1000 genomes]
rs8079616	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8080662	0.84[ASN][1000 genomes]
rs978263	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9807087	0.91[ASN][1000 genomes]
rs9890691	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9903692	0.83[ASN][1000 genomes]
rs9909933	0.81[ASN][1000 genomes]
rs9910516	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	esv1007058	chr17:46188741-46200367	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10853097	CBX1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46186000-46198600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:46186200-46198600	Weak transcription	Fetal Brain Male	brain
3	chr17:46186200-46203600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr17:46186400-46198600	Weak transcription	Small Intestine	intestine
5	chr17:46186400-46198800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr17:46187600-46198400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr17:46188200-46201200	Strong transcription	Fetal Intestine Small	intestine
8	chr17:46188200-46207400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr17:46188400-46201400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr17:46189000-46202600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr17:46189200-46199000	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr17:46189400-46198600	Strong transcription	Brain Anterior Caudate	brain
13	chr17:46189400-46204200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr17:46189600-46198800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr17:46189600-46200600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr17:46189600-46201800	Strong transcription	Fetal Muscle Leg	muscle
17	chr17:46189800-46202000	Strong transcription	Fetal Stomach	stomach
18	chr17:46190000-46201400	Strong transcription	Lung	lung
19	chr17:46190000-46204800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr17:46190200-46201600	Strong transcription	Liver	Liver
21	chr17:46190400-46200600	Strong transcription	Fetal Muscle Trunk	muscle
22	chr17:46190400-46201600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr17:46190400-46205000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr17:46190800-46201400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr17:46191200-46201800	Strong transcription	Adipose Nuclei	Adipose
26	chr17:46191200-46220800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr17:46191600-46204600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr17:46191800-46201200	Strong transcription	Fetal Intestine Large	intestine
29	chr17:46191800-46201600	Strong transcription	Primary T cells from cord blood	blood
30	chr17:46191800-46204600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr17:46192000-46201000	Strong transcription	Left Ventricle	heart
32	chr17:46192000-46201200	Strong transcription	Placenta	Placenta
33	chr17:46192200-46199200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr17:46192200-46200200	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr17:46192200-46201200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr17:46192200-46201600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr17:46192200-46202400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr17:46192400-46200000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr17:46192400-46200600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr17:46192400-46200800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr17:46192400-46201000	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr17:46192400-46201000	Strong transcription	Thymus	Thymus
43	chr17:46192400-46201200	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr17:46192400-46201200	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr17:46192400-46201200	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr17:46192400-46201400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr17:46192400-46201400	Strong transcription	Fetal Thymus	thymus
48	chr17:46192400-46201600	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr17:46192400-46201600	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr17:46192400-46204800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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