Variant report

Variant	rs12488164
Chromosome Location	chr3:119173989-119173990
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119171366..119177327-chr3:119178101..119183743,11	MCF-7	breast:
2	chr3:119150195..119152799-chr3:119173269..119174905,2	K562	blood:
3	chr3:119137060..119139008-chr3:119172885..119175851,2	K562	blood:
4	chr3:119173608..119175156-chr3:119189458..119191935,2	K562	blood:

Variant related genes	Relation type
ENSG00000176142	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1000199	0.81[ASN][1000 genomes]
rs1001674	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10511391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12485665	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12487191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12487982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12488535	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12489912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12490630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12492315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12492609	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12492859	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12493175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12493326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12493328	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12493965	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12494114	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12494943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12495539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12495580	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12495749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12496277	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12497394	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13062955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13078312	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13078816	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13081067	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13081197	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13090653	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13093049	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13094625	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13096213	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16829838	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16829850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16829853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16829865	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16829896	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1997341	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2282170	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2282174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3088258	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33958792	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34023538	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34208844	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34250818	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34468255	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34746401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34834687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34849715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35084408	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35169866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35282209	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35488908	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35563598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35761622	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3732420	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6641	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6796981	0.83[EUR][1000 genomes]
rs71325376	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71325378	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71325380	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71618009	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119147000-119179000	Strong transcription	Osteobl	bone
2	chr3:119147200-119180400	Weak transcription	Stomach Mucosa	stomach
3	chr3:119147400-119179200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:119148800-119175400	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr3:119148800-119180400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:119149400-119179000	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:119149400-119181000	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:119149400-119181600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:119150200-119179000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:119150400-119180200	Strong transcription	Fetal Intestine Large	intestine
11	chr3:119150600-119175400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:119150600-119180800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:119152000-119178000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:119152000-119179800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:119152200-119178800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:119152200-119179400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:119154000-119181800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:119157000-119177000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:119158000-119180000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr3:119158800-119180000	Strong transcription	Adipose Nuclei	Adipose
21	chr3:119158800-119180000	Strong transcription	Dnd41	blood
22	chr3:119159800-119179400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:119159800-119180800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:119160400-119179400	Strong transcription	Duodenum Mucosa	Duodenum
25	chr3:119160400-119180200	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr3:119160600-119180000	Strong transcription	HUVEC	blood vessel
27	chr3:119160600-119180800	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:119160800-119179400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:119161000-119179000	Strong transcription	Liver	Liver
30	chr3:119161000-119180800	Weak transcription	Fetal Brain Male	brain
31	chr3:119161200-119179600	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr3:119161800-119175600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:119161800-119180000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:119161800-119180400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:119162200-119174200	Strong transcription	GM12878-XiMat	blood
36	chr3:119162600-119181000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:119162800-119179200	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr3:119163200-119178200	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:119163200-119179800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr3:119163200-119180400	Strong transcription	HSMM	muscle
41	chr3:119163200-119180800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:119163200-119180800	Strong transcription	Placenta	Placenta
43	chr3:119163200-119181000	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr3:119163400-119178600	Strong transcription	Stomach Smooth Muscle	stomach
45	chr3:119163400-119180400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr3:119163400-119180800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:119163400-119180800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:119163400-119180800	Strong transcription	Fetal Muscle Trunk	muscle
49	chr3:119163400-119181200	Strong transcription	Fetal Thymus	thymus
50	chr3:119163600-119179000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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