Variant report

Variant	rs2657881
Chromosome Location	chr12:56862886-56862887
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56692603..56696463-chr12:56860417..56864951,9	K562	blood:
2	chr12:56727342..56729039-chr12:56862325..56863904,2	K562	blood:
3	chr12:56708282..56711640-chr12:56860573..56864710,5	K562	blood:
4	chr12:56650600..56652635-chr12:56861995..56863652,2	MCF-7	breast:
5	chr12:56860897..56864227-chr12:56865813..56869854,5	MCF-7	breast:
6	chr12:56752523..56755343-chr12:56862151..56864248,2	MCF-7	breast:
7	chr12:56841526..56846188-chr12:56861608..56864760,4	K562	blood:
8	chr12:56650281..56653173-chr12:56862365..56864133,2	K562	blood:
9	chr12:56694327..56696089-chr12:56861619..56863910,2	MCF-7	breast:
10	chr12:56862344..56864045-chr12:56880136..56881879,2	MCF-7	breast:
11	chr12:56862204..56864692-chr12:56870931..56873632,2	MCF-7	breast:
12	chr12:56650076..56651919-chr12:56861997..56863613,2	MCF-7	breast:
13	chr12:56683757..56687058-chr12:56862106..56864198,3	K562	blood:
14	chr12:56861952..56864525-chr12:57027360..57030112,3	MCF-7	breast:
15	chr12:56692603..56696463-chr12:56860417..56864951,8	K562	blood:
16	chr12:56839562..56844740-chr12:56860089..56866019,9	MCF-7	breast:
17	chr12:56708394..56711484-chr12:56860870..56863906,7	MCF-7	breast:
18	chr12:56861539..56863714-chr12:57023540..57025612,3	MCF-7	breast:
19	chr12:56707342..56711323-chr12:56861186..56863695,3	MCF-7	breast:
20	chr12:56582327..56583849-chr12:56861847..56864785,2	MCF-7	breast:
21	chr12:56752241..56754348-chr12:56862536..56866569,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000139645	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000135423	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000076108	Chromatin interaction
ENSG00000144785	Chromatin interaction
ENSG00000135473	Chromatin interaction
ENSG00000170581	Chromatin interaction
ENSG00000257727	Chromatin interaction
ENSG00000111602	Chromatin interaction
ENSG00000257303	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12306723	1.00[TSI][hapmap]
rs12318580	1.00[TSI][hapmap]
rs12321709	1.00[TSI][hapmap]
rs2657914	1.00[ASW][hapmap];0.81[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs774040	1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv1052713	chr12:56848036-56917602	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2657881	PXDN	trans	lymphoblastoid	seeQTL
rs2657881	SCGB3A1	trans	lymphoblastoid	seeQTL
rs2657881	PRRX1	trans	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56861200-56863000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:56861600-56863000	Active TSS	Duodenum Mucosa	Duodenum
3	chr12:56861600-56863000	Active TSS	Fetal Intestine Small	intestine
4	chr12:56861600-56863200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:56861600-56863200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:56861600-56863200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:56861800-56863000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:56861800-56863000	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr12:56861800-56863000	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr12:56861800-56863000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:56861800-56863000	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr12:56861800-56863000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:56861800-56863000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:56861800-56863000	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr12:56861800-56863000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:56861800-56863000	Active TSS	Muscle Satellite Cultured Cells	--
17	chr12:56861800-56863000	Active TSS	Brain Germinal Matrix	brain
18	chr12:56861800-56863000	Active TSS	Brain Hippocampus Middle	brain
19	chr12:56861800-56863000	Active TSS	Colon Smooth Muscle	Colon
20	chr12:56861800-56863000	Active TSS	Esophagus	oesophagus
21	chr12:56861800-56863000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr12:56861800-56863000	Active TSS	Fetal Intestine Large	intestine
23	chr12:56861800-56863000	Active TSS	Fetal Stomach	stomach
24	chr12:56861800-56863000	Active TSS	Pancreas	Pancrea
25	chr12:56861800-56863000	Active TSS	Psoas Muscle	Psoas
26	chr12:56861800-56863000	Active TSS	Rectal Smooth Muscle	rectum
27	chr12:56861800-56863000	Active TSS	Right Ventricle	heart
28	chr12:56861800-56863000	Active TSS	A549	lung
29	chr12:56861800-56863000	Active TSS	GM12878-XiMat	blood
30	chr12:56861800-56863000	Active TSS	Hela-S3	cervix
31	chr12:56861800-56863000	Active TSS	HMEC	breast
32	chr12:56861800-56863000	Active TSS	NHDF-Ad	bronchial
33	chr12:56861800-56863000	Active TSS	NHLF	lung
34	chr12:56861800-56863000	Active TSS	Osteobl	bone
35	chr12:56861800-56863200	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr12:56861800-56863200	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr12:56861800-56863200	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr12:56861800-56863200	Active TSS	Ovary	ovary
39	chr12:56861800-56863400	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr12:56861800-56863400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:56861800-56863400	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr12:56861800-56863400	Active TSS	HSMM	muscle
43	chr12:56861800-56863600	Active TSS	Fetal Kidney	kidney
44	chr12:56862000-56863000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr12:56862000-56863000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr12:56862000-56863000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr12:56862000-56863000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:56862000-56863000	Active TSS	Fetal Brain Male	brain
49	chr12:56862000-56863000	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr12:56862000-56863000	Active TSS	Small Intestine	intestine

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