Variant report

Variant	rs3857503
Chromosome Location	chr6:163828698-163828699
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	chr6:163828630..163831846-chr6:163832456..163835653,4	MCF-7	breast:
2	chr6:163824877..163830472-chr6:163836413..163839637,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270419	Chromatin interaction
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11760168	0.83[AMR][1000 genomes]
rs11962088	0.81[ASN][1000 genomes]
rs13202116	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13202733	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13204052	0.90[AMR][1000 genomes];0.94[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]
rs1737321	0.81[ASN][1000 genomes]
rs1737328	0.87[ASN][1000 genomes]
rs1764009	0.81[ASN][1000 genomes]
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]
rs2784872	0.81[ASN][1000 genomes]
rs2784875	0.81[ASN][1000 genomes]
rs4263561	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709713	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4709716	0.84[ASN][1000 genomes]
rs55779730	0.89[ASN][1000 genomes]
rs56062115	0.85[ASN][1000 genomes]
rs6455897	0.89[AMR][1000 genomes]
rs6908317	0.81[ASN][1000 genomes]
rs6921172	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6927805	0.81[ASN][1000 genomes]
rs6929436	0.82[ASN][1000 genomes]
rs6939218	0.88[ASN][1000 genomes]
rs718878	0.81[ASN][1000 genomes]
rs718879	0.81[ASN][1000 genomes]
rs73013582	0.88[ASN][1000 genomes]
rs73013591	0.82[ASN][1000 genomes]
rs9364687	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
11	nsv605193	chr6:163824864-163835490	Flanking Active TSS Weak transcription Active TSS Enhancers 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
12	nsv605194	chr6:163824864-163836293	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv605195	chr6:163824864-163836634	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163827000-163832000	Weak transcription	Gastric	stomach
2	chr6:163827200-163830800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:163827200-163832000	Weak transcription	Placenta	Placenta
4	chr6:163827200-163832000	Weak transcription	Lung	lung
5	chr6:163827200-163833600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:163827200-163833600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:163827200-163833800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:163827200-163834200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:163827200-163834200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:163827200-163834200	Weak transcription	Spleen	Spleen
11	chr6:163827400-163828800	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr6:163827400-163829000	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr6:163827400-163829600	Weak transcription	A549	lung
14	chr6:163827400-163830400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr6:163827400-163830800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:163827400-163832400	Weak transcription	Left Ventricle	heart
17	chr6:163827400-163833000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr6:163827400-163833400	Weak transcription	HSMM	muscle
19	chr6:163827400-163833600	Weak transcription	Psoas Muscle	Psoas
20	chr6:163827400-163833600	Weak transcription	Right Atrium	heart
21	chr6:163827400-163833800	Weak transcription	Aorta	Aorta
22	chr6:163827600-163828800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr6:163827600-163828800	Enhancers	Brain Angular Gyrus	brain
24	chr6:163827600-163828800	Enhancers	Brain Hippocampus Middle	brain
25	chr6:163827600-163828800	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr6:163827600-163828800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:163827600-163828800	Enhancers	NHDF-Ad	bronchial
28	chr6:163827600-163829000	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr6:163827600-163829200	Enhancers	Brain Cingulate Gyrus	brain
30	chr6:163827600-163829600	Enhancers	HepG2	liver
31	chr6:163827600-163832000	Weak transcription	HSMMtube	muscle
32	chr6:163827600-163833400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr6:163827600-163833400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr6:163827600-163833400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr6:163827600-163833400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:163827600-163833400	Weak transcription	Fetal Lung	lung
37	chr6:163827600-163833400	Weak transcription	Fetal Stomach	stomach
38	chr6:163827600-163833400	Weak transcription	NHLF	lung
39	chr6:163827600-163833800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:163827800-163828800	Enhancers	Brain Anterior Caudate	brain
41	chr6:163827800-163830000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr6:163827800-163830400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr6:163827800-163833400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr6:163827800-163833400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:163827800-163833400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:163827800-163833400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:163827800-163833400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:163828000-163833200	Weak transcription	HUVEC	blood vessel
49	chr6:163828000-163833600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr6:163828200-163829200	Enhancers	Monocytes-CD14+_RO01746	blood

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