Variant report

Variant	rs66588280
Chromosome Location	chr6:88431206-88431207
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	chr6:88408898..88411861-chr6:88430189..88432233,3	K562	blood:
2	chr6:88410379..88413746-chr6:88430806..88436396,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135334	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12190308	0.81[ASN][1000 genomes]
rs16879704	0.89[EUR][1000 genomes]
rs16879736	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28381530	0.85[EUR][1000 genomes]
rs3763177	0.86[EUR][1000 genomes]
rs41273297	0.86[EUR][1000 genomes]
rs56400749	0.85[EUR][1000 genomes]
rs58060521	0.89[EUR][1000 genomes]
rs59131518	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59774543	0.86[EUR][1000 genomes]
rs60082015	0.82[EUR][1000 genomes]
rs66502414	0.89[EUR][1000 genomes]
rs66965134	0.89[EUR][1000 genomes]
rs67063139	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs67575319	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67700862	0.89[EUR][1000 genomes]
rs67993159	0.89[EUR][1000 genomes]
rs68082038	0.88[EUR][1000 genomes]
rs715207	0.85[EUR][1000 genomes]
rs72906514	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72924342	0.89[EUR][1000 genomes]
rs7747792	0.89[EUR][1000 genomes]
rs7748286	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7776049	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450782	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758068	chr6:88358988-88441473	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv2759454	chr6:88358988-88441473	Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88412800-88432600	Weak transcription	Brain Angular Gyrus	brain
2	chr6:88420200-88436800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:88422200-88432400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr6:88424400-88432400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:88424600-88432400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:88424600-88432400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:88424600-88432400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr6:88424600-88432400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:88424600-88432800	Weak transcription	Fetal Thymus	thymus
10	chr6:88424600-88439200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:88425200-88432200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:88425200-88432200	Weak transcription	HSMM	muscle
13	chr6:88425200-88432400	Weak transcription	Hela-S3	cervix
14	chr6:88426800-88432000	Enhancers	A549	lung
15	chr6:88427000-88432000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr6:88427200-88432400	Weak transcription	NH-A	brain
17	chr6:88427200-88432600	Weak transcription	Brain Anterior Caudate	brain
18	chr6:88427400-88431600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr6:88427400-88432200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr6:88427400-88432800	Weak transcription	Fetal Muscle Leg	muscle
21	chr6:88427400-88432800	Weak transcription	Left Ventricle	heart
22	chr6:88427600-88432400	Weak transcription	Brain Hippocampus Middle	brain
23	chr6:88427600-88432800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr6:88427600-88439400	Weak transcription	Right Atrium	heart
25	chr6:88427800-88432800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:88428000-88432400	Weak transcription	HepG2	liver
27	chr6:88428800-88431800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr6:88429000-88432800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr6:88429000-88432800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr6:88429200-88432000	Weak transcription	K562	blood
31	chr6:88429200-88432200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:88429200-88432400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr6:88429200-88432800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:88429400-88431800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:88429400-88432000	Weak transcription	GM12878-XiMat	blood
36	chr6:88429400-88432000	Weak transcription	HMEC	breast
37	chr6:88429400-88432000	Weak transcription	NHLF	lung
38	chr6:88429400-88432200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr6:88429400-88432200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr6:88429400-88432400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr6:88429400-88432400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:88429400-88432800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr6:88429400-88432800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr6:88429400-88432800	Weak transcription	Placenta	Placenta
45	chr6:88429400-88434800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr6:88429400-88439400	Weak transcription	Esophagus	oesophagus
47	chr6:88429600-88432000	Weak transcription	Primary hematopoietic stem cells	blood
48	chr6:88429600-88432200	Weak transcription	NHEK	skin
49	chr6:88429600-88432400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:88429600-88432400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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