Variant report

Variant	rs12700667
Chromosome Location	chr7:25901639-25901640
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr7:25900891..25903409-chr7:25932154..25934177,2	K562	blood:
2	chr7:25896710..25899572-chr7:25900375..25902445,3	MCF-7	breast:
3	chr7:25900989..25903469-chr7:26394737..26397654,2	K562	blood:
4	chr7:25901385..25904121-chr7:25989908..25991928,2	MCF-7	breast:
5	chr7:25901348..25903877-chr7:25904726..25907059,2	K562	blood:
6	chr7:25900544..25903827-chr7:25911333..25915801,5	K562	blood:
7	chr7:25900551..25904078-chr7:26238740..26241514,6	K562	blood:
8	chr7:25900279..25902478-chr7:26238832..26241424,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000122565	Chromatin interaction
ENSG00000122566	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10225976	0.85[EUR][1000 genomes]
rs10232819	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10241659	0.85[EUR][1000 genomes]
rs10261019	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10271088	0.83[EUR][1000 genomes]
rs10271460	0.85[EUR][1000 genomes]
rs10274306	0.85[EUR][1000 genomes]
rs10951112	0.88[ASN][1000 genomes]
rs11976790	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12535837	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1376527	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1451382	0.85[EUR][1000 genomes]
rs1451383	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1451385	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2893220	0.85[EUR][1000 genomes]
rs3902751	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4722526	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4722527	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4722528	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4722529	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4722530	0.88[ASN][1000 genomes]
rs4722531	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56376645	0.86[EUR][1000 genomes]
rs60643312	0.85[EUR][1000 genomes]
rs61140461	0.85[EUR][1000 genomes]
rs62447896	0.85[EUR][1000 genomes]
rs6461887	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6958350	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7782246	0.83[EUR][1000 genomes]
rs7782292	0.85[EUR][1000 genomes]
rs7793216	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7798431	0.85[EUR][1000 genomes]
rs979165	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs994505	0.85[AFR][1000 genomes]
rs9987000	0.88[ASN][1000 genomes]

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	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
2	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv830928	chr7:25820147-25965014	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Endometriosis	21151130	GWAS catalog
Endometriosis	23104006	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12700667	CCDC126	cis	parietal	SCAN
rs12700667	SKAP2	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25900000-25901800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
2	chr7:25900000-25902800	Active TSS	NHDF-Ad	bronchial
3	chr7:25900000-25903800	Active TSS	K562	blood
4	chr7:25900400-25902600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:25900800-25902800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr7:25901000-25902400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
7	chr7:25901200-25901800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:25901200-25901800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr7:25901200-25901800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr7:25901200-25901800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:25901200-25901800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr7:25901200-25902000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:25901200-25902000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr7:25901200-25902000	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr7:25901200-25902000	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
16	chr7:25901200-25902600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:25901200-25902600	Bivalent Enhancer	Fetal Heart	heart
18	chr7:25901400-25901800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr7:25901400-25901800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:25901400-25901800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
21	chr7:25901400-25901800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
22	chr7:25901400-25901800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
23	chr7:25901400-25901800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:25901400-25901800	Bivalent/Poised TSS	Placenta	Placenta
25	chr7:25901400-25901800	Active TSS	HMEC	breast
26	chr7:25901400-25901800	Active TSS	HSMM	muscle
27	chr7:25901400-25901800	Flanking Active TSS	NHEK	skin
28	chr7:25901400-25902000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
29	chr7:25901400-25902000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr7:25901400-25902000	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
31	chr7:25901400-25902000	Active TSS	HSMMtube	muscle
32	chr7:25901400-25902000	Active TSS	NHLF	lung
33	chr7:25901400-25902200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
34	chr7:25901400-25902200	Active TSS	Colonic Mucosa	Colon
35	chr7:25901400-25902400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
36	chr7:25901400-25902600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr7:25901400-25902600	Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr7:25901400-25902600	Bivalent/Poised TSS	GM12878-XiMat	blood
39	chr7:25901400-25902800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
40	chr7:25901400-25903000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
41	chr7:25901400-25903000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
42	chr7:25901600-25901800	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr7:25901600-25901800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr7:25901600-25901800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr7:25901600-25901800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
46	chr7:25901600-25901800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
47	chr7:25901600-25901800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
48	chr7:25901600-25901800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr7:25901600-25901800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
50	chr7:25901600-25901800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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