Variant report

Variant	rs12086880
Chromosome Location	chr1:45964413-45964414
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr1:45964375-45964493	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45804114..45807301-chr1:45961577..45967419,8	K562	blood:
2	chr1:45283510..45287262-chr1:45964108..45968951,6	K562	blood:
3	chr1:45806085..45807923-chr1:45963911..45966246,2	MCF-7	breast:
4	chr1:45963397..45969763-chr1:46047572..46053150,23	K562	blood:
5	chr1:45963437..45971807-chr1:46047572..46053150,22	K562	blood:
6	chr1:45265558..45267516-chr1:45964222..45967034,2	K562	blood:
7	chr1:45954905..45960579-chr1:45960652..45966878,10	K562	blood:
8	chr1:45964150..45967582-chr1:46014583..46018871,5	K562	blood:
9	chr1:45284392..45287262-chr1:45964108..45967526,3	K562	blood:

No data

Variant related genes	Relation type
MMACHC	TF binding region
CCDC163P	TF binding region
ENSG00000117448	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000070759	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000173846	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11211127	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11211144	1.00[AMR][1000 genomes]
rs11211148	1.00[AMR][1000 genomes]
rs11211153	1.00[AMR][1000 genomes]
rs11211154	1.00[AMR][1000 genomes]
rs11211155	1.00[AMR][1000 genomes]
rs11211156	1.00[AMR][1000 genomes]
rs11211167	1.00[AMR][1000 genomes]
rs12057167	1.00[AMR][1000 genomes]
rs12060056	1.00[AMR][1000 genomes]
rs12061890	1.00[AMR][1000 genomes]
rs12063380	1.00[AMR][1000 genomes]
rs12064908	1.00[AMR][1000 genomes]
rs12067882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12070146	1.00[AMR][1000 genomes]
rs12070177	1.00[AMR][1000 genomes]
rs12073045	1.00[AMR][1000 genomes]
rs12073047	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12073132	1.00[AMR][1000 genomes]
rs12077112	1.00[AMR][1000 genomes]
rs12080482	1.00[AMR][1000 genomes]
rs12081121	1.00[AMR][1000 genomes]
rs12082672	1.00[AMR][1000 genomes]
rs12085372	1.00[AMR][1000 genomes]
rs12088810	1.00[AMR][1000 genomes]
rs12091335	1.00[AMR][1000 genomes]
rs12091360	1.00[AMR][1000 genomes]
rs12093444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12094011	1.00[AMR][1000 genomes]
rs12097914	1.00[AMR][1000 genomes]
rs16832540	1.00[AMR][1000 genomes]
rs16832550	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16832553	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16832557	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1691225	1.00[AMR][1000 genomes]
rs1691226	1.00[AMR][1000 genomes]
rs1691227	1.00[AMR][1000 genomes]
rs1762087	1.00[AMR][1000 genomes]
rs2782489	1.00[AMR][1000 genomes]
rs28532613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28607905	1.00[AMR][1000 genomes]
rs35067820	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35808563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs486346	1.00[AMR][1000 genomes]
rs505175	1.00[AMR][1000 genomes]
rs506094	1.00[AMR][1000 genomes]
rs525706	1.00[AMR][1000 genomes]
rs622296	1.00[AMR][1000 genomes]
rs635446	1.00[AMR][1000 genomes]
rs665014	1.00[AMR][1000 genomes]
rs668289	1.00[AMR][1000 genomes]
rs669417	1.00[AMR][1000 genomes]
rs680267	1.00[AMR][1000 genomes]
rs7550744	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
5	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
6	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
7	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
8	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45956800-45964600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:45956800-45964800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:45956800-45964800	Weak transcription	Spleen	Spleen
4	chr1:45956800-45965000	Weak transcription	Gastric	stomach
5	chr1:45956800-45974000	Weak transcription	Small Intestine	intestine
6	chr1:45957000-45964600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:45957000-45964800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:45957400-45964600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:45957400-45965200	Weak transcription	HSMM	muscle
10	chr1:45957600-45964600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:45957600-45964600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:45957600-45964600	Weak transcription	Ovary	ovary
13	chr1:45957600-45964600	Weak transcription	Thymus	Thymus
14	chr1:45957600-45964600	Weak transcription	Osteobl	bone
15	chr1:45957600-45964800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:45957600-45964800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:45957600-45964800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr1:45957600-45965000	Weak transcription	Psoas Muscle	Psoas
19	chr1:45957800-45964600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:45957800-45964600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:45957800-45964800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:45957800-45964800	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:45957800-45965000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:45957800-45965000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr1:45958000-45964600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:45958000-45964600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:45958000-45964600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:45958000-45964600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:45958000-45964800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr1:45958000-45964800	Weak transcription	Adipose Nuclei	Adipose
31	chr1:45958800-45964600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr1:45958800-45964800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr1:45958800-45964800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:45959200-45964600	Weak transcription	Colon Smooth Muscle	Colon
35	chr1:45959200-45964600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr1:45961000-45964800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:45961200-45964800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:45962400-45964800	Weak transcription	Primary T cells from cord blood	blood
39	chr1:45962400-45964800	Weak transcription	Esophagus	oesophagus
40	chr1:45962400-45965000	Weak transcription	Right Atrium	heart
41	chr1:45962600-45964600	Weak transcription	HMEC	breast
42	chr1:45962600-45964600	Weak transcription	NHEK	skin
43	chr1:45962600-45964800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:45962600-45964800	Weak transcription	Lung	lung
45	chr1:45962600-45965000	Weak transcription	Left Ventricle	heart
46	chr1:45963000-45964800	Weak transcription	Placenta	Placenta
47	chr1:45963200-45965200	Weak transcription	Aorta	Aorta
48	chr1:45964000-45964800	Enhancers	Brain Hippocampus Middle	brain
49	chr1:45964000-45964800	Enhancers	Brain Substantia Nigra	brain
50	chr1:45964000-45964800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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