Variant report

Variant	rs2016762
Chromosome Location	chr6:82525799-82525800
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:82525422-82525946	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr6:82525433-82526001	H1-neurons	neurons:	n/a	n/a
3	SIN3AK20	chr6:82525453-82526800	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:82475840..82480204-chr6:82524356..82527900,4	MCF-7	breast:
2	chr6:82507285..82509817-chr6:82524544..82526925,2	MCF-7	breast:
3	chr6:82458586..82464036-chr6:82521971..82527096,10	MCF-7	breast:
4	chr6:82495383..82498182-chr6:82525424..82528036,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224995	TF binding region
ENSG00000112773	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs6924771	0.81[EUR][1000 genomes]
rs7749739	0.81[EUR][1000 genomes]
rs9344223	0.88[EUR][1000 genomes]
rs9361860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs964909	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[EUR][1000 genomes]
rs999567	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.90[TSI][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830712	chr6:82491029-82654531	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2016762	RORA	trans	lymphoblastoid	seeQTL
rs2016762	TPBG	cis	lymphoblastoid	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:82517200-82530600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:82519200-82528800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:82522800-82531400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr6:82523000-82530000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:82523200-82528000	Weak transcription	Primary B cells from cord blood	blood
6	chr6:82523400-82527800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:82523400-82528000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr6:82523800-82527400	Enhancers	Hela-S3	cervix
9	chr6:82523800-82532600	Enhancers	Stomach Mucosa	stomach
10	chr6:82524000-82528000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr6:82524000-82528200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr6:82524200-82526400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:82524600-82526400	Enhancers	Placenta	Placenta
14	chr6:82524600-82528800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:82524800-82528600	Weak transcription	Right Atrium	heart
16	chr6:82524800-82528800	Weak transcription	Gastric	stomach
17	chr6:82524800-82529000	Weak transcription	NHLF	lung
18	chr6:82525000-82526000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:82525000-82526200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:82525000-82526200	Weak transcription	NHDF-Ad	bronchial
21	chr6:82525000-82527200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:82525000-82528400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:82525000-82529000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:82525200-82527400	Enhancers	HepG2	liver
25	chr6:82525200-82528200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:82525200-82529000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr6:82525400-82528000	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr6:82525600-82527800	Weak transcription	Monocytes-CD14+_RO01746	blood

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