Variant report

Variant	rs240421
Chromosome Location	chr6:75952697-75952698
allele	A/T
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	chr6:75952178..75953795-chr6:76311805..76314377,2	K562	blood:
6	chr6:75951699..75955124-chr6:75992599..75996025,9	K562	blood:
7	chr6:75951485..75954328-chr6:75992401..75995008,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112695	Chromatin interaction
ENSG00000119899	Chromatin interaction
ENSG00000112701	Chromatin interaction
ENSG00000112697	Chromatin interaction
ENSG00000225793	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1203210	0.84[EUR][1000 genomes]
rs1203215	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12176508	0.86[EUR][1000 genomes]
rs1407733	0.94[EUR][1000 genomes]
rs1407734	0.94[EUR][1000 genomes]
rs1474847	0.88[EUR][1000 genomes]
rs171261	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs173274	0.83[EUR][1000 genomes]
rs187067	0.83[EUR][1000 genomes]
rs1967709	0.94[EUR][1000 genomes]
rs1998454	0.90[EUR][1000 genomes]
rs240363	0.94[EUR][1000 genomes]
rs240365	0.94[EUR][1000 genomes]
rs240366	0.94[EUR][1000 genomes]
rs240370	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs240394	0.83[EUR][1000 genomes]
rs240395	0.83[EUR][1000 genomes]
rs240399	0.83[EUR][1000 genomes]
rs240408	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs240411	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs240418	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs240420	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs240422	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240433	0.94[EUR][1000 genomes]
rs3756791	0.90[EUR][1000 genomes]
rs3777510	0.90[EUR][1000 genomes]
rs409536	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs415416	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs431116	0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs436898	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs588691	0.94[EUR][1000 genomes]
rs601846	0.94[EUR][1000 genomes]
rs656182	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs743003	0.94[EUR][1000 genomes]
rs743004	0.90[EUR][1000 genomes]
rs743005	0.94[EUR][1000 genomes]
rs7768671	0.90[EUR][1000 genomes]
rs910523	0.94[EUR][1000 genomes]
rs9293997	0.88[EUR][1000 genomes]
rs9443160	0.90[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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75944200-75953000	Weak transcription	Stomach Mucosa	stomach
2	chr6:75944400-75952800	Weak transcription	Aorta	Aorta
3	chr6:75944400-75952800	Weak transcription	Brain Angular Gyrus	brain
4	chr6:75944400-75952800	Weak transcription	Ovary	ovary
5	chr6:75945600-75952800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:75947600-75952800	Weak transcription	Fetal Heart	heart
7	chr6:75949200-75952800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:75949200-75952800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:75949200-75952800	Weak transcription	Esophagus	oesophagus
10	chr6:75949400-75952800	Weak transcription	Brain Substantia Nigra	brain
11	chr6:75949600-75952800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr6:75949600-75952800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:75949800-75952800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:75949800-75952800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:75950000-75952800	Weak transcription	Brain Hippocampus Middle	brain
16	chr6:75950000-75952800	Weak transcription	Colonic Mucosa	Colon
17	chr6:75950000-75952800	Weak transcription	HSMM	muscle
18	chr6:75950200-75952800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:75950600-75952800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:75950600-75952800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr6:75951200-75952800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:75951200-75954000	Active TSS	GM12878-XiMat	blood
23	chr6:75951400-75952800	Enhancers	Primary B cells from peripheral blood	blood
24	chr6:75951400-75952800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr6:75951400-75952800	Weak transcription	Brain Anterior Caudate	brain
26	chr6:75951600-75952800	Weak transcription	Colon Smooth Muscle	Colon
27	chr6:75951600-75953800	Active TSS	Hela-S3	cervix
28	chr6:75951800-75952800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr6:75951800-75954200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:75952000-75952800	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr6:75952000-75952800	Enhancers	Thymus	Thymus
32	chr6:75952000-75953000	Weak transcription	Small Intestine	intestine
33	chr6:75952000-75953600	Active TSS	K562	blood
34	chr6:75952000-75954000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:75952000-75954400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr6:75952000-75954400	Active TSS	A549	lung
37	chr6:75952000-75954400	Active TSS	NHLF	lung
38	chr6:75952200-75952800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr6:75952200-75952800	Weak transcription	Fetal Brain Male	brain
40	chr6:75952200-75952800	Weak transcription	Gastric	stomach
41	chr6:75952200-75952800	Weak transcription	Pancreas	Pancrea
42	chr6:75952200-75952800	Weak transcription	Psoas Muscle	Psoas
43	chr6:75952200-75952800	Flanking Active TSS	Dnd41	blood
44	chr6:75952200-75952800	Active TSS	HepG2	liver
45	chr6:75952200-75953400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:75952200-75953800	Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr6:75952200-75954000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:75952200-75954000	Active TSS	Muscle Satellite Cultured Cells	--
49	chr6:75952200-75954000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:75952200-75954000	Active TSS	Duodenum Mucosa	Duodenum

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