Variant report

Variant	rs12139412
Chromosome Location	chr1:179925399-179925400
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr1:179924982-179925551	K562	blood:	n/a	chr1:179925333-179925343 chr1:179925332-179925346
2	MXI1	chr1:179924305-179925470	K562	blood:	n/a	n/a
3	POLR2A	chr1:179923020-179925612	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:179844528..179853403-chr1:179920065..179927793,25	K562	blood:
2	chr1:179845348..179847730-chr1:179923811..179926342,3	MCF-7	breast:
3	chr1:179921069..179927710-chr1:179937007..179944258,10	K562	blood:
4	chr1:179924257..179926025-chr1:179973260..179975368,2	K562	blood:
5	chr1:179849016..179853452-chr1:179922333..179928502,16	K562	blood:
6	chr1:179847679..179853408-chr1:179922379..179926886,15	MCF-7	breast:
7	chr1:179923952..179925915-chr1:180137472..180139404,2	MCF-7	breast:
8	chr1:179884565..179886596-chr1:179924353..179925912,2	MCF-7	breast:
9	chr1:179909218..179916721-chr1:179922197..179926382,9	K562	blood:
10	chr1:179924119..179925876-chr1:179942859..179944489,2	MCF-7	breast:
11	chr1:179923898..179926923-chr1:180121889..180124249,4	MCF-7	breast:
12	chr1:179923938..179925991-chr1:180198274..180200305,2	MCF-7	breast:
13	chr1:179842979..179846933-chr1:179922588..179926684,5	K562	blood:
14	chr1:179889749..179892017-chr1:179923918..179925424,2	MCF-7	breast:
15	chr1:179906513..179911873-chr1:179922155..179925771,5	K562	blood:
16	chr1:179923424..179925663-chr1:179935642..179938173,4	MCF-7	breast:
17	chr1:179924485..179926237-chr20:44016912..44018546,2	MCF-7	breast:
18	chr1:179848142..179854405-chr1:179919774..179927189,17	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000260360	TF binding region
ENSG00000116260	Chromatin interaction
ENSG00000232880	Chromatin interaction
ENSG00000272906	Chromatin interaction
ENSG00000121454	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000169905	Chromatin interaction
ENSG00000261831	Chromatin interaction
ENSG00000235145	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10442618	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10494524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913920	0.84[EUR][1000 genomes]
rs12118985	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12120418	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12121834	0.92[ASN][1000 genomes]
rs12121845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12123139	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12123201	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12125556	0.92[ASN][1000 genomes]
rs12125693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12125893	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12130397	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12130479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12130673	0.84[EUR][1000 genomes]
rs12130675	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131200	0.84[EUR][1000 genomes]
rs12132694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133136	0.84[EUR][1000 genomes]
rs12134536	0.92[ASN][1000 genomes]
rs12135751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135828	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12138201	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12138974	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12139323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139761	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12140235	0.92[ASN][1000 genomes]
rs12140589	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12140868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12141817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144275	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12145411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16843139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16854997	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16855014	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16855019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855049	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855052	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855070	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16855099	0.84[ASN][1000 genomes]
rs16855103	0.84[ASN][1000 genomes]
rs16855107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16855110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16855125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16855130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16855144	0.84[ASN][1000 genomes]
rs16855259	0.84[ASN][1000 genomes]
rs16855268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16855270	0.92[ASN][1000 genomes]
rs16855286	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs16855289	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17299006	0.84[EUR][1000 genomes]
rs3856048	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41267622	0.84[ASN][1000 genomes]
rs4266842	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4278337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4460595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57165548	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58316647	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs58463801	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58749862	0.92[ASN][1000 genomes]
rs58844263	0.84[ASN][1000 genomes]
rs59132689	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60064848	0.84[ASN][1000 genomes]
rs60895715	0.84[ASN][1000 genomes]
rs60927554	0.84[ASN][1000 genomes]
rs60972670	0.92[ASN][1000 genomes]
rs60976015	0.84[ASN][1000 genomes]
rs61014689	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61242295	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73032352	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032390	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73032397	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73034408	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73034486	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73039990	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73039999	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73040001	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525395	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7556630	0.85[ASN][1000 genomes]
rs9699897	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9701232	0.84[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	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179922600-179925400	Active TSS	Colonic Mucosa	Colon
2	chr1:179922600-179926000	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr1:179922800-179925400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:179922800-179925400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:179922800-179925400	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr1:179922800-179925400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:179922800-179925400	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr1:179922800-179925400	Active TSS	Fetal Muscle Trunk	muscle
9	chr1:179922800-179925600	Active TSS	H1 Cell Line	embryonic stem cell
10	chr1:179922800-179925600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:179922800-179925600	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr1:179922800-179925800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:179922800-179925800	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr1:179922800-179925800	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr1:179922800-179925800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:179922800-179925800	Active TSS	Right Ventricle	heart
17	chr1:179922800-179926000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:179922800-179926000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:179922800-179926000	Active TSS	Psoas Muscle	Psoas
20	chr1:179922800-179926800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:179922800-179926800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:179922800-179927000	Active TSS	Fetal Intestine Large	intestine
23	chr1:179923000-179925400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:179923000-179925400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:179923000-179925400	Active TSS	Aorta	Aorta
26	chr1:179923000-179925800	Active TSS	Fetal Muscle Leg	muscle
27	chr1:179923000-179926000	Active TSS	Ovary	ovary
28	chr1:179923200-179925400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:179923200-179925400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:179923200-179925400	Active TSS	A549	lung
31	chr1:179923200-179925400	Active TSS	HSMMtube	muscle
32	chr1:179923200-179925600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:179923200-179925600	Active TSS	Fetal Stomach	stomach
34	chr1:179923200-179925600	Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr1:179923200-179925800	Active TSS	Brain Anterior Caudate	brain
36	chr1:179923200-179925800	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr1:179923200-179925800	Active TSS	Stomach Smooth Muscle	stomach
38	chr1:179923200-179925800	Active TSS	Thymus	Thymus
39	chr1:179923200-179925800	Active TSS	NHDF-Ad	bronchial
40	chr1:179923200-179926200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:179923200-179926200	Active TSS	Muscle Satellite Cultured Cells	--
42	chr1:179923200-179926600	Active TSS	NHLF	lung
43	chr1:179923400-179925400	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr1:179923400-179925800	Active TSS	Fetal Intestine Small	intestine
45	chr1:179923600-179926600	Active TSS	HMEC	breast
46	chr1:179923600-179926600	Active TSS	K562	blood
47	chr1:179923600-179928000	Active TSS	GM12878-XiMat	blood
48	chr1:179923800-179925400	Active TSS	Hela-S3	cervix
49	chr1:179924400-179925400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr1:179924400-179925400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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