Variant report

Variant	rs6456727
Chromosome Location	chr6:26471155-26471156
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26464821..26467283-chr6:26470555..26474076,4	MCF-7	breast:
2	chr6:26467959..26470668-chr6:26470770..26473697,4	MCF-7	breast:
3	chr6:26467030..26468631-chr6:26469753..26471368,2	MCF-7	breast:
4	chr6:26420100..26422498-chr6:26469157..26471386,2	K562	blood:
5	chr6:26432568..26435135-chr6:26469851..26472610,2	K562	blood:
6	chr6:26456463..26458175-chr6:26469301..26471348,2	MCF-7	breast:
7	chr6:26470620..26472220-chr6:26474706..26477657,2	MCF-7	breast:
8	chr6:26470613..26473867-chr6:26476951..26479626,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000124549	Chromatin interaction
ENSG00000112763	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs13195047	0.86[EUR][1000 genomes]
rs16891717	0.91[EUR][1000 genomes]
rs2093169	0.91[EUR][1000 genomes]
rs2273558	0.85[ASN][1000 genomes]
rs34313099	0.87[EUR][1000 genomes]
rs3734544	0.91[EUR][1000 genomes]
rs3757150	0.91[EUR][1000 genomes]
rs3799380	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4518487	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56296968	0.91[EUR][1000 genomes]
rs6456728	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6924727	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6926677	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6933213	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6941920	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7756567	0.91[EUR][1000 genomes]
rs7773938	0.91[EUR][1000 genomes]
rs9348719	0.91[EUR][1000 genomes]
rs9348720	0.91[EUR][1000 genomes]
rs9358944	0.91[EUR][1000 genomes]
rs9358945	0.91[EUR][1000 genomes]
rs9358946	0.91[EUR][1000 genomes]
rs9358947	0.91[EUR][1000 genomes]
rs9358948	0.91[EUR][1000 genomes]
rs9366658	0.91[EUR][1000 genomes]
rs9379880	0.90[EUR][1000 genomes]
rs9467772	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
4	nsv482836	chr6:26352883-26520964	Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv482407	chr6:26369320-26550148	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
6	nsv1031238	chr6:26428314-26471596	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1031938	chr6:26467182-26501897	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6456727	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs6456727	BTN2A1	Cis_1M	lymphoblastoid	RTeQTL
rs6456727	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26460000-26471400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:26461600-26471200	Strong transcription	Fetal Intestine Small	intestine
3	chr6:26461600-26471600	Strong transcription	Fetal Stomach	stomach
4	chr6:26461600-26471600	Weak transcription	Right Atrium	heart
5	chr6:26462000-26471200	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr6:26462000-26471200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:26462000-26471200	Strong transcription	Fetal Intestine Large	intestine
8	chr6:26462000-26471400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:26462000-26472000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:26462200-26471600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:26462800-26471200	Strong transcription	Lung	lung
12	chr6:26464600-26471600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:26464600-26471600	Weak transcription	Psoas Muscle	Psoas
14	chr6:26465600-26471400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr6:26466400-26471600	Weak transcription	Fetal Brain Male	brain
16	chr6:26466600-26473800	Weak transcription	Fetal Heart	heart
17	chr6:26467200-26472800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:26467200-26473800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr6:26467400-26471600	Weak transcription	Fetal Kidney	kidney
20	chr6:26467400-26471600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr6:26467600-26471600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr6:26468000-26471600	Weak transcription	Stomach Mucosa	stomach
23	chr6:26468400-26471600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr6:26468600-26471600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:26469000-26471600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr6:26469000-26473200	Weak transcription	Hela-S3	cervix
27	chr6:26469200-26471600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:26469200-26471600	Weak transcription	Colonic Mucosa	Colon
29	chr6:26469200-26472800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr6:26469400-26471600	Weak transcription	Gastric	stomach
31	chr6:26469400-26473800	Weak transcription	Ovary	ovary
32	chr6:26469600-26471200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:26469600-26471600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:26469600-26471600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:26469600-26471600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr6:26469600-26471600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:26469600-26471600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr6:26469600-26471600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr6:26469600-26471600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr6:26469600-26471600	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr6:26469600-26471600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:26469600-26471600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:26469600-26471600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr6:26469600-26471600	Weak transcription	Adipose Nuclei	Adipose
45	chr6:26469600-26471600	Weak transcription	Aorta	Aorta
46	chr6:26469600-26471600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr6:26469600-26471600	Weak transcription	Brain Hippocampus Middle	brain
48	chr6:26469600-26471600	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr6:26469600-26471600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:26469600-26471600	Weak transcription	Brain Substantia Nigra	brain

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