Variant report

Variant	rs240420
Chromosome Location	chr6:75952171-75952172
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:75952010..75957701-chr6:75957886..75965537,16	MCF-7	breast:
2	chr6:74363322..74365404-chr6:75950708..75953547,2	MCF-7	breast:
3	chr6:75949911..75955499-chr6:75993041..75995715,6	MCF-7	breast:
4	chr6:75951366..75953542-chr6:75992434..75995845,4	K562	blood:
5	chr6:75951699..75955124-chr6:75992599..75996025,9	K562	blood:
6	chr6:75951485..75954328-chr6:75992401..75995008,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112697	Chromatin interaction
ENSG00000119899	Chromatin interaction
ENSG00000225793	Chromatin interaction
ENSG00000112695	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1203215	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12176508	0.81[EUR][1000 genomes]
rs1407733	0.88[EUR][1000 genomes]
rs1407734	0.88[EUR][1000 genomes]
rs1474847	0.83[EUR][1000 genomes]
rs171261	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1967709	0.88[EUR][1000 genomes]
rs1998454	0.84[EUR][1000 genomes]
rs240363	0.88[EUR][1000 genomes]
rs240365	0.88[EUR][1000 genomes]
rs240366	0.88[EUR][1000 genomes]
rs240370	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs240408	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs240411	0.87[EUR][1000 genomes]
rs240418	0.85[EUR][1000 genomes]
rs240421	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs240422	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs240433	0.88[EUR][1000 genomes]
rs3756791	0.84[EUR][1000 genomes]
rs3777510	0.84[EUR][1000 genomes]
rs409536	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs415416	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs431116	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs436898	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs588691	0.88[EUR][1000 genomes]
rs601846	0.88[EUR][1000 genomes]
rs656182	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs743003	0.88[EUR][1000 genomes]
rs743004	0.84[EUR][1000 genomes]
rs743005	0.88[EUR][1000 genomes]
rs7768671	0.84[EUR][1000 genomes]
rs910523	0.88[EUR][1000 genomes]
rs9293997	0.83[EUR][1000 genomes]
rs9443160	0.84[EUR][1000 genomes]

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	nsv1016804	chr6:75775846-76188585	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538310	chr6:75775846-76188585	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv463155	chr6:75789526-75980419	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv603762	chr6:75789526-75980419	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1024079	chr6:75848556-76238519	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
8	nsv603763	chr6:75923605-76009426	Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75940400-75952600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:75944200-75953000	Weak transcription	Stomach Mucosa	stomach
3	chr6:75944400-75952800	Weak transcription	Aorta	Aorta
4	chr6:75944400-75952800	Weak transcription	Brain Angular Gyrus	brain
5	chr6:75944400-75952800	Weak transcription	Ovary	ovary
6	chr6:75945600-75952800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:75946200-75952600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:75946400-75952600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr6:75947200-75952200	Weak transcription	Fetal Brain Female	brain
10	chr6:75947600-75952800	Weak transcription	Fetal Heart	heart
11	chr6:75949200-75952200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr6:75949200-75952800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:75949200-75952800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:75949200-75952800	Weak transcription	Esophagus	oesophagus
15	chr6:75949400-75952400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:75949400-75952400	Weak transcription	Primary T cells from cord blood	blood
17	chr6:75949400-75952400	Weak transcription	Fetal Kidney	kidney
18	chr6:75949400-75952800	Weak transcription	Brain Substantia Nigra	brain
19	chr6:75949600-75952800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr6:75949600-75952800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr6:75949800-75952200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr6:75949800-75952400	Weak transcription	Fetal Stomach	stomach
23	chr6:75949800-75952600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr6:75949800-75952800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:75949800-75952800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:75950000-75952200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:75950000-75952200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:75950000-75952600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr6:75950000-75952600	Weak transcription	Fetal Lung	lung
30	chr6:75950000-75952600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr6:75950000-75952800	Weak transcription	Brain Hippocampus Middle	brain
32	chr6:75950000-75952800	Weak transcription	Colonic Mucosa	Colon
33	chr6:75950000-75952800	Weak transcription	HSMM	muscle
34	chr6:75950200-75952200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr6:75950200-75952600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:75950200-75952600	Weak transcription	HSMMtube	muscle
37	chr6:75950200-75952800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:75950400-75952200	Weak transcription	NH-A	brain
39	chr6:75950400-75952600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr6:75950600-75952800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:75950600-75952800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr6:75950800-75952400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr6:75950800-75952600	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr6:75951000-75952200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:75951000-75952200	Enhancers	Duodenum Mucosa	Duodenum
46	chr6:75951000-75952200	Enhancers	Fetal Brain Male	brain
47	chr6:75951000-75952400	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr6:75951000-75952400	Weak transcription	HMEC	breast
49	chr6:75951000-75952600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr6:75951200-75952200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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