Variant report

Variant	rs4263561
Chromosome Location	chr6:163822296-163822297
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:163820034..163822360-chr6:163835389..163837208,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11760168	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11962088	0.88[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs13202116	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13202733	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13204052	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1336223	0.81[ASN][1000 genomes]
rs1336224	0.81[ASN][1000 genomes]
rs1336225	0.81[ASN][1000 genomes]
rs1414724	0.81[ASN][1000 genomes]
rs1591536	0.81[ASN][1000 genomes]
rs16894934	0.81[ASN][1000 genomes]
rs16895015	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs1737319	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs1737321	0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1737322	0.85[JPT][hapmap]
rs1737324	0.83[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs1737328	0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs17591955	0.83[CHB][hapmap]
rs1764009	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1764010	0.83[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs1764011	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs1764015	0.81[ASN][1000 genomes]
rs1764019	0.81[ASN][1000 genomes]
rs1764020	0.87[ASN][1000 genomes]
rs2064226	0.81[ASN][1000 genomes]
rs2065857	0.81[ASN][1000 genomes]
rs2143358	0.90[CHD][hapmap];0.90[JPT][hapmap]
rs2294698	0.94[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap]
rs2294703	0.83[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs2294706	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs2294709	0.94[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs2784872	0.81[ASN][1000 genomes]
rs2784875	0.81[ASN][1000 genomes]
rs3763197	0.83[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs3857503	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3857504	0.90[JPT][hapmap]
rs3904720	0.90[JPT][hapmap]
rs4709713	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4709716	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs4709717	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs55779730	0.89[ASN][1000 genomes]
rs56062115	0.85[ASN][1000 genomes]
rs6455897	0.94[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6908317	0.81[ASN][1000 genomes]
rs6921172	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6927805	0.81[ASN][1000 genomes]
rs6929436	0.82[ASN][1000 genomes]
rs6931903	0.83[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs6939218	0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs715020	0.89[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs718878	0.81[ASN][1000 genomes]
rs718879	0.81[ASN][1000 genomes]
rs73013582	0.88[ASN][1000 genomes]
rs73013591	0.82[ASN][1000 genomes]
rs7758706	0.83[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs7771996	0.85[YRI][hapmap]
rs7772756	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs9346960	0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs9347760	0.89[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap]
rs9364687	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9364689	0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs9364691	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs9364692	0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1791729	chr6:163814557-163836689	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv1839403	chr6:163822296-163835490	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1793461	chr6:163822296-163836634	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv1794611	chr6:163822296-163836689	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv1796475	chr6:163822296-163836689	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv1797016	chr6:163822296-163836689	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv1801202	chr6:163822296-163836689	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv1801861	chr6:163822296-163836689	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4263561	SESTD1	trans	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163809800-163825600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:163818000-163822600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:163818000-163826800	Weak transcription	Gastric	stomach
4	chr6:163818200-163825600	Weak transcription	Lung	lung
5	chr6:163818200-163826200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:163818200-163826800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:163818400-163825200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr6:163818400-163825400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:163818400-163825400	Weak transcription	Right Atrium	heart
10	chr6:163818600-163823400	Weak transcription	Fetal Heart	heart
11	chr6:163818800-163825800	Weak transcription	Colon Smooth Muscle	Colon
12	chr6:163818800-163826400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:163819000-163824000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:163819400-163822600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:163819600-163822400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:163819800-163825000	Enhancers	Placenta	Placenta
17	chr6:163820000-163825600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:163820200-163823000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr6:163820200-163823000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr6:163820200-163823200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:163820200-163825600	Weak transcription	Spleen	Spleen
22	chr6:163820200-163825800	Weak transcription	Psoas Muscle	Psoas
23	chr6:163820200-163826000	Weak transcription	Brain Germinal Matrix	brain
24	chr6:163820200-163826000	Weak transcription	Fetal Brain Female	brain
25	chr6:163820200-163826800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:163820400-163822400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr6:163820400-163822600	Weak transcription	Brain Anterior Caudate	brain
28	chr6:163820400-163822600	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr6:163820400-163823000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr6:163820400-163824600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr6:163820400-163824600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr6:163820400-163824800	Weak transcription	Brain Angular Gyrus	brain
33	chr6:163820400-163825600	Weak transcription	Fetal Muscle Leg	muscle
34	chr6:163820400-163826000	Weak transcription	Ovary	ovary
35	chr6:163820400-163826800	Weak transcription	GM12878-XiMat	blood
36	chr6:163820600-163825400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:163820600-163826600	Weak transcription	Fetal Brain Male	brain
38	chr6:163820800-163823400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr6:163820800-163825600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr6:163821000-163822400	Weak transcription	Brain Substantia Nigra	brain
41	chr6:163821200-163823200	Weak transcription	Brain Hippocampus Middle	brain
42	chr6:163821400-163824600	Enhancers	H1 Cell Line	embryonic stem cell
43	chr6:163821400-163827000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:163821800-163823000	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr6:163821800-163823400	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr6:163821800-163824400	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr6:163822000-163823000	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr6:163822000-163825400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:163822000-163825400	Weak transcription	Adipose Nuclei	Adipose
50	chr6:163822200-163822600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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