Variant report

Variant	rs12476390
Chromosome Location	chr2:86181427-86181428
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:86179766..86181607-chr2:86220908..86223298,2	K562	blood:
2	chr2:86160879..86165285-chr2:86176010..86181999,6	MCF-7	breast:
3	chr2:86178306..86181703-chr2:86184579..86188621,5	MCF-7	breast:
4	chr2:86112970..86117219-chr2:86178282..86182179,5	MCF-7	breast:
5	chr2:86112745..86122516-chr2:86175080..86185190,27	MCF-7	breast:
6	chr2:85820787..85822313-chr2:86179412..86182366,2	K562	blood:
7	chr2:86137885..86140851-chr2:86180033..86182072,2	MCF-7	breast:
8	chr2:86181209..86184209-chr2:86184954..86187247,3	K562	blood:
9	chr2:86179973..86182095-chr2:86197318..86199407,2	MCF-7	breast:
10	chr2:86135754..86137623-chr2:86180466..86183254,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000232504	Chromatin interaction
ENSG00000115525	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10181091	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10181916	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10183118	0.82[EUR][1000 genomes]
rs10186005	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189191	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10198260	0.92[ASN][1000 genomes]
rs1020095	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11890514	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891625	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12470643	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12472588	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714161	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12714163	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12714164	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12714165	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13000793	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13397189	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1438153	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1438155	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561330	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1866242	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866243	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1866245	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4346389	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4480982	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4514874	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832018	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4832020	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6547651	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706720	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708525	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713002	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6728146	0.81[EUR][1000 genomes]
rs6737454	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597264	0.87[ASN][1000 genomes]
rs934830	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12476390	IMMT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86175000-86183600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:86178800-86181800	Enhancers	A549	lung
3	chr2:86178800-86188200	Enhancers	Fetal Muscle Leg	muscle
4	chr2:86179200-86182200	Weak transcription	Esophagus	oesophagus
5	chr2:86179200-86183600	Enhancers	Pancreas	Pancrea
6	chr2:86179200-86183800	Enhancers	Stomach Mucosa	stomach
7	chr2:86179800-86181600	Enhancers	Brain Angular Gyrus	brain
8	chr2:86179800-86181800	Enhancers	Brain Hippocampus Middle	brain
9	chr2:86179800-86182000	Enhancers	Brain Substantia Nigra	brain
10	chr2:86180000-86181800	Enhancers	Brain Anterior Caudate	brain
11	chr2:86180000-86181800	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr2:86180000-86181800	Enhancers	Lung	lung
13	chr2:86180000-86182000	Enhancers	Fetal Lung	lung
14	chr2:86180000-86183400	Enhancers	Fetal Muscle Trunk	muscle
15	chr2:86180200-86181800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:86180200-86183000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr2:86180200-86187600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:86180400-86181800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:86180600-86181600	Weak transcription	Liver	Liver
20	chr2:86180600-86181600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:86180600-86182000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:86180600-86184200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:86180800-86181600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:86180800-86182400	Enhancers	HepG2	liver
25	chr2:86180800-86184000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr2:86180800-86184400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:86180800-86188600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:86181000-86182200	Weak transcription	NHEK	skin
29	chr2:86181000-86182400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:86181000-86183000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:86181000-86183600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:86181000-86183800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:86181000-86186600	Weak transcription	K562	blood
34	chr2:86181400-86181800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:86181400-86182000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:86181400-86182200	Enhancers	Gastric	stomach

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