Variant report

Variant	rs6905408
Chromosome Location	chr6:29633775-29633776
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	chr6:29619372..29622160-chr6:29632758..29634460,2	K562	blood:
2	chr6:29633426..29635000-chr6:29636787..29639241,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204655	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2071652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071653	0.83[ASN][1000 genomes]
rs3095291	0.84[ASN][1000 genomes]
rs3117290	0.84[ASN][1000 genomes]
rs3131854	0.83[ASN][1000 genomes]
rs9257927	0.91[AMR][1000 genomes]
rs9257932	0.85[EUR][1000 genomes]
rs9257940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9257953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9257986	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258004	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9258130	0.83[ASN][1000 genomes]
rs9258132	0.83[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	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6905408	HLA-F	cis	lymphoblastoid	seeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29625000-29663600	Weak transcription	Right Atrium	heart
2	chr6:29629800-29634400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:29630400-29633800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:29630600-29633800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:29630800-29634200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:29630800-29643200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:29631400-29640200	Weak transcription	NHEK	skin
8	chr6:29631800-29633800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:29631800-29635200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:29632000-29633800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr6:29632000-29634600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:29632000-29636200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:29632000-29638600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:29632600-29634400	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr6:29633200-29633800	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr6:29633400-29634200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr6:29633400-29634400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr6:29633400-29634600	Enhancers	H1 Cell Line	embryonic stem cell
19	chr6:29633400-29634600	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr6:29633400-29635200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:29633400-29635600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:29633400-29635600	Genic enhancers	Brain Substantia Nigra	brain
23	chr6:29633400-29636000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr6:29633400-29636400	Enhancers	Fetal Heart	heart
25	chr6:29633600-29634200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr6:29633600-29634400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
27	chr6:29633600-29634600	Genic enhancers	Brain Angular Gyrus	brain
28	chr6:29633600-29634600	Enhancers	Brain Anterior Caudate	brain
29	chr6:29633600-29635000	Genic enhancers	Brain Cingulate Gyrus	brain
30	chr6:29633600-29635000	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr6:29633600-29635400	Genic enhancers	Brain Hippocampus Middle	brain
32	chr6:29633600-29636600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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