Variant report

Variant	rs201001
Chromosome Location	chr6:27808899-27808900
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:27808559-27808953	K562	blood:	n/a	n/a
2	POLR2A	chr6:27803736-27809014	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:79474511..79476714-chr6:27807469..27810310,2	K562	blood:
2	chr6:27142668..27145341-chr6:27807841..27810817,2	K562	blood:
3	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:
4	chr6:27100116..27102377-chr6:27807509..27809506,3	MCF-7	breast:
5	chr6:26031272..26033892-chr6:27807337..27809404,2	K562	blood:
6	chr6:27807137..27809779-chr6:28070833..28072678,2	K562	blood:
7	chr6:27111071..27119431-chr6:27801399..27810552,22	K562	blood:
8	chr6:26154851..26161490-chr6:27803982..27809302,10	MCF-7	breast:

No data

Variant related genes	Relation type
HIST1H2AK	TF binding region
ENSG00000184825	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000158373	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs200486	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs200502	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs200503	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs200504	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs200956	0.94[ASN][1000 genomes]
rs200969	0.86[ASN][1000 genomes]
rs200978	0.89[ASN][1000 genomes]
rs200991	0.97[AFR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs200994	0.91[ASN][1000 genomes]
rs201000	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs201004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs573179	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
3	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
4	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
5	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs201001	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs201001	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs201001	AL022393.7	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27807600-27816600	Weak transcription	Pancreas	Pancrea
2	chr6:27807800-27812800	Weak transcription	HSMM	muscle
3	chr6:27807800-27814800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:27808000-27812800	Weak transcription	Primary B cells from cord blood	blood
5	chr6:27808000-27813000	Weak transcription	HSMMtube	muscle
6	chr6:27808000-27815800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:27808000-27819000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:27808000-27822400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr6:27808000-27831800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:27808200-27809400	Weak transcription	Fetal Thymus	thymus
11	chr6:27808200-27810600	Weak transcription	NH-A	brain
12	chr6:27808200-27815000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:27808200-27815200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:27808200-27817200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr6:27808200-27818800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr6:27808200-27830600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:27808400-27809400	Weak transcription	GM12878-XiMat	blood
18	chr6:27808400-27809600	Weak transcription	A549	lung
19	chr6:27808400-27810400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr6:27808400-27810600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:27808400-27811800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:27808400-27812200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr6:27808400-27813000	Weak transcription	Liver	Liver
24	chr6:27808400-27814400	Weak transcription	HepG2	liver
25	chr6:27808400-27814800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:27808400-27815000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:27808400-27815000	Weak transcription	NHDF-Ad	bronchial
28	chr6:27808400-27815600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:27808400-27818000	Weak transcription	Hela-S3	cervix
30	chr6:27808800-27809000	Enhancers	Psoas Muscle	Psoas
31	chr6:27808800-27809800	Weak transcription	Dnd41	blood
32	chr6:27808800-27810200	Genic enhancers	K562	blood

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