Variant report

Variant	rs7563870
Chromosome Location	chr2:73051636-73051637
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	chr1:149857730..149860576-chr2:73051525..73053981,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184270	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000178096	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10187814	0.90[AMR][1000 genomes]
rs10188019	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10195520	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10205532	0.90[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10469964	1.00[AMR][1000 genomes]
rs11883986	0.90[AMR][1000 genomes]
rs11891034	1.00[MEX][hapmap]
rs11902280	0.90[AMR][1000 genomes]
rs12105464	0.89[AMR][1000 genomes]
rs13390314	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13391151	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13397183	0.90[AMR][1000 genomes]
rs13399612	0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13405645	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13405937	0.90[AMR][1000 genomes]
rs13416510	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs13426439	0.87[AFR][1000 genomes]
rs28581818	0.90[AMR][1000 genomes]
rs6546784	0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6738020	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7585242	0.90[AMR][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	nsv834259	chr2:72941118-73114106	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7563870	PRRX1	trans	lymphoblastoid	seeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73036600-73051800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:73037200-73051800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:73038400-73052000	Weak transcription	Aorta	Aorta
4	chr2:73045200-73051800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:73046200-73051800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:73049400-73051800	Active TSS	Right Ventricle	heart
7	chr2:73049400-73052200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:73049800-73051800	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr2:73049800-73051800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:73050000-73052000	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr2:73050000-73052200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:73050200-73051800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr2:73050200-73051800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:73050200-73051800	Weak transcription	Dnd41	blood
15	chr2:73050600-73051800	Enhancers	Pancreas	Pancrea
16	chr2:73050800-73051800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:73050800-73052000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:73050800-73052000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:73050800-73052200	Enhancers	Primary T cells fromperipheralblood	blood
20	chr2:73050800-73052200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:73051000-73051800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr2:73051000-73052400	Flanking Active TSS	NHEK	skin
23	chr2:73051200-73051800	Enhancers	Fetal Stomach	stomach
24	chr2:73051200-73051800	Enhancers	Psoas Muscle	Psoas
25	chr2:73051200-73051800	Enhancers	Stomach Mucosa	stomach
26	chr2:73051200-73051800	Enhancers	NH-A	brain
27	chr2:73051200-73051800	Enhancers	NHLF	lung
28	chr2:73051200-73051800	Enhancers	Osteobl	bone
29	chr2:73051200-73052000	Bivalent Enhancer	Primary T cells from cord blood	blood
30	chr2:73051200-73052000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:73051200-73052000	Enhancers	Gastric	stomach
32	chr2:73051200-73052000	Enhancers	Ovary	ovary
33	chr2:73051200-73052000	Enhancers	Small Intestine	intestine
34	chr2:73051200-73052200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:73051200-73052200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:73051200-73052200	Flanking Active TSS	Brain Germinal Matrix	brain
37	chr2:73051200-73052200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
38	chr2:73051200-73052200	Flanking Active TSS	HMEC	breast
39	chr2:73051200-73052400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr2:73051200-73052600	Flanking Active TSS	Hela-S3	cervix
41	chr2:73051200-73053200	Active TSS	H9 Cell Line	embryonic stem cell
42	chr2:73051400-73051800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr2:73051400-73051800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:73051400-73051800	Weak transcription	Lung	lung
45	chr2:73051400-73051800	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr2:73051400-73051800	Enhancers	HSMM	muscle
47	chr2:73051400-73052000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr2:73051400-73052000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr2:73051400-73052000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr2:73051400-73052000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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