Variant report

Variant	rs2886070
Chromosome Location	chr1:155973971-155973972
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	JUN	chr1:155973093-155974060	K562	blood:	n/a	chr1:155973425-155973433
2	GATA2	chr1:155973361-155973979	SH-SY5Y	brain:	n/a	chr1:155973394-155973403

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:155902774..155905937-chr1:155970220..155974829,6	K562	blood:
2	chr1:155950118..155953012-chr1:155973513..155975361,2	K562	blood:
3	chr1:155972459..155975057-chr1:155976597..155981157,4	MCF-7	breast:
4	chr1:155902817..155905494-chr1:155972290..155974046,2	MCF-7	breast:
5	chr1:155973245..155975433-chr1:156026948..156029277,2	MCF-7	breast:
6	chr1:155970847..155975108-chr1:155988635..155992129,4	MCF-7	breast:
7	chr1:155912056..155914225-chr1:155973245..155974818,2	MCF-7	breast:
8	chr1:155959078..155960932-chr1:155973199..155976085,2	K562	blood:

No data

Variant related genes	Relation type
ARHGEF2	TF binding region
ENSG00000116584	Chromatin interaction
ENSG00000163479	Chromatin interaction
ENSG00000132680	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10908486	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11577179	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11582305	0.85[AMR][1000 genomes]
rs12032631	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12043212	0.92[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12128541	1.00[CEU][hapmap];0.80[CHB][hapmap];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1475766	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17381047	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17385065	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1966243	0.83[AMR][1000 genomes]
rs2095402	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2297792	1.00[CEU][hapmap];0.80[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2364400	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2364401	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2364409	0.83[ASN][1000 genomes]
rs34126883	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34444588	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34995046	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4330912	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4661079	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6668204	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7517202	0.95[AMR][1000 genomes];0.84[EUR][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	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2886070	RIT1	cis	cerebellum	SCAN
rs2886070	YY1AP1	cis	cerebellum	SCAN
rs2886070	SNX27	cis	parietal	SCAN
rs2886070	PRUNE	cis	cerebellum	SCAN
rs2886070	SYT11	cis	parietal	SCAN
rs2886070	ROBLD3	cis	parietal	SCAN
rs2886070	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs2886070	UBQLN4	trans	parietal	SCAN
rs2886070	SPRR3	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155959200-155978200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:155959400-155976600	Weak transcription	Aorta	Aorta
3	chr1:155959800-155974600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:155961200-155974600	Weak transcription	Lung	lung
5	chr1:155966200-155976600	Weak transcription	Brain Substantia Nigra	brain
6	chr1:155966200-155976800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:155966400-155978200	Weak transcription	Left Ventricle	heart
8	chr1:155966400-155978400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:155967000-155976600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:155967000-155976600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:155967000-155978400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:155970400-155974000	Flanking Active TSS	Hela-S3	cervix
13	chr1:155970600-155975000	Enhancers	HMEC	breast
14	chr1:155970800-155978200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:155971000-155974600	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr1:155971400-155974000	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr1:155971400-155978600	Weak transcription	Brain Angular Gyrus	brain
18	chr1:155971400-155978600	Weak transcription	NHDF-Ad	bronchial
19	chr1:155971600-155978400	Weak transcription	Ovary	ovary
20	chr1:155971600-155978400	Weak transcription	Right Ventricle	heart
21	chr1:155971600-155978600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:155971800-155974800	Weak transcription	Brain Anterior Caudate	brain
23	chr1:155971800-155976600	Weak transcription	Placenta	Placenta
24	chr1:155971800-155976600	Weak transcription	Pancreas	Pancrea
25	chr1:155971800-155976800	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:155971800-155978400	Weak transcription	Osteobl	bone
27	chr1:155971800-155978600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:155972000-155974600	Weak transcription	Fetal Heart	heart
29	chr1:155972000-155976600	Weak transcription	Liver	Liver
30	chr1:155972000-155976600	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr1:155972000-155978600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr1:155972200-155974600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:155972200-155976600	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr1:155972200-155976600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:155972200-155976800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:155972400-155974600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:155972400-155974600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:155972400-155974800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:155972400-155976800	Weak transcription	Adipose Nuclei	Adipose
40	chr1:155972400-155978400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:155972400-155978400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:155972400-155978400	Weak transcription	Fetal Kidney	kidney
43	chr1:155972400-155978600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:155972600-155975200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:155972600-155976200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:155972600-155976600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:155972800-155974600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:155972800-155976600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr1:155972800-155978400	Weak transcription	HSMMtube	muscle
50	chr1:155973000-155974000	Active TSS	Colonic Mucosa	Colon

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