Variant report

Variant	rs12666961
Chromosome Location	chr7:25895685-25895686
allele	C/T
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:25889250..25893042-chr7:25894239..25896921,6	K562	blood:
2	chr7:25889535..25891445-chr7:25893362..25896566,3	MCF-7	breast:
3	chr7:25894376..25896556-chr7:25914929..25917518,2	K562	blood:
4	chr7:25895415..25898294-chr7:25979885..25982093,2	K562	blood:
5	chr7:25775918..25778772-chr7:25894489..25897280,2	K562	blood:
6	chr7:25894376..25896420-chr7:25914591..25917518,2	K562	blood:
7	chr7:25163504..25166316-chr7:25894348..25896748,3	K562	blood:
8	chr7:25163578..25166316-chr7:25895123..25897377,2	K562	blood:
9	chr7:25894784..25898696-chr7:26228733..26232018,3	MCF-7	breast:
10	chr7:25878624..25881558-chr7:25895080..25897783,3	K562	blood:
11	chr7:25163296..25164829-chr7:25893486..25896365,2	MCF-7	breast:
12	chr7:25878624..25881558-chr7:25895267..25897783,2	K562	blood:
13	chr7:25891320..25893042-chr7:25894595..25897680,4	K562	blood:
14	chr7:25894581..25899810-chr7:26238604..26243593,7	K562	blood:
15	chr7:25893947..25899810-chr7:26238759..26243593,6	K562	blood:
16	chr7:25893800..25898221-chr7:26239034..26243289,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000122565	Chromatin interaction
ENSG00000122566	Chromatin interaction
ENSG00000172115	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10225976	0.88[ASN][1000 genomes]
rs10238703	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10241634	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10241659	0.84[ASN][1000 genomes]
rs10242536	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10245353	0.83[EUR][1000 genomes]
rs10260677	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10262483	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10267498	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10271088	0.85[ASN][1000 genomes]
rs10271460	0.84[ASN][1000 genomes]
rs10274306	0.84[ASN][1000 genomes]
rs10282436	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1055144	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10951112	0.89[EUR][1000 genomes]
rs11770186	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1451382	0.85[ASN][1000 genomes]
rs1451385	0.84[CEU][hapmap]
rs2391168	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28392961	0.83[EUR][1000 genomes]
rs28473292	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28858973	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2893220	0.84[ASN][1000 genomes]
rs2893221	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35766302	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4141278	0.84[EUR][1000 genomes]
rs41469349	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4722530	0.91[EUR][1000 genomes]
rs56376645	0.89[ASN][1000 genomes]
rs57246313	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60643312	0.86[ASN][1000 genomes]
rs61140461	0.84[ASN][1000 genomes]
rs62447896	0.83[ASN][1000 genomes]
rs7782246	0.84[ASN][1000 genomes]
rs7782292	0.84[ASN][1000 genomes]
rs7798002	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7798130	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7798431	0.85[ASN][1000 genomes]
rs9987000	0.91[EUR][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

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25892800-25896200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:25893400-25896400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr7:25893400-25898000	Active TSS	NHDF-Ad	bronchial
4	chr7:25894000-25896000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:25894000-25896800	Active TSS	Stomach Smooth Muscle	stomach
6	chr7:25894000-25897000	Active TSS	K562	blood
7	chr7:25894000-25897200	Active TSS	Aorta	Aorta
8	chr7:25894000-25897400	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr7:25894000-25897800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr7:25894200-25895800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr7:25894200-25895800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr7:25894200-25896000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr7:25894200-25896200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
14	chr7:25894200-25897200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr7:25894200-25897600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr7:25894400-25895800	Bivalent/Poised TSS	NH-A	brain
17	chr7:25894400-25896000	ZNF genes & repeats	GM12878-XiMat	blood
18	chr7:25894400-25896200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
19	chr7:25894600-25895800	Active TSS	Rectal Mucosa Donor 31	rectum
20	chr7:25894600-25896200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
21	chr7:25894600-25896200	Bivalent Enhancer	Fetal Thymus	thymus
22	chr7:25894600-25897200	Active TSS	NHLF	lung
23	chr7:25894800-25895800	Active TSS	Fetal Kidney	kidney
24	chr7:25894800-25897400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr7:25895000-25895800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr7:25895000-25896000	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
27	chr7:25895000-25896000	Bivalent/Poised TSS	Fetal Stomach	stomach
28	chr7:25895000-25896200	Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr7:25895000-25896400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr7:25895000-25897400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:25895000-25897600	Active TSS	Psoas Muscle	Psoas
32	chr7:25895000-25898800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr7:25895200-25895800	Bivalent Enhancer	Fetal Lung	lung
34	chr7:25895200-25896000	Active TSS	Colonic Mucosa	Colon
35	chr7:25895200-25896400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr7:25895200-25897400	Active TSS	HSMM	muscle
37	chr7:25895400-25895800	Active TSS	Adipose Nuclei	Adipose
38	chr7:25895400-25895800	Active TSS	HSMMtube	muscle
39	chr7:25895400-25896000	Active TSS	Colon Smooth Muscle	Colon
40	chr7:25895400-25897200	Active TSS	Rectal Smooth Muscle	rectum
41	chr7:25895400-25897600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr7:25895400-25897600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
43	chr7:25895600-25895800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
44	chr7:25895600-25895800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr7:25895600-25895800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
46	chr7:25895600-25895800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
47	chr7:25895600-25895800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
48	chr7:25895600-25895800	Active TSS	Osteobl	bone
49	chr7:25895600-25896000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr7:25895600-25896000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

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