Variant report

Variant	rs12500272
Chromosome Location	chr4:119658434-119658435
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:119657007..119658653-chr4:119665008..119667662,2	MCF-7	breast:
2	chr4:119653222..119655642-chr4:119658116..119660847,2	K562	blood:

Variant related genes	Relation type
ENSG00000150961	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10518322	0.87[AMR][1000 genomes]
rs10518323	0.87[AMR][1000 genomes]
rs10518324	0.87[AMR][1000 genomes]
rs11098449	0.83[AMR][1000 genomes]
rs11098450	0.87[AMR][1000 genomes]
rs11722833	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11730993	0.88[AMR][1000 genomes]
rs11736024	0.81[ASN][1000 genomes]
rs12505513	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12509236	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12509654	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12649666	0.81[ASN][1000 genomes]
rs13109947	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13109966	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13114964	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13120798	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13130107	0.96[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs17050423	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs298976	0.91[EUR][1000 genomes]
rs298977	0.91[EUR][1000 genomes]
rs298980	0.96[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs298981	0.91[EUR][1000 genomes]
rs298989	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs298990	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs298993	0.92[EUR][1000 genomes]
rs298997	0.91[EUR][1000 genomes]
rs299002	0.90[EUR][1000 genomes]
rs299003	0.90[EUR][1000 genomes]
rs299004	0.90[EUR][1000 genomes]
rs34371874	0.91[EUR][1000 genomes]
rs34384498	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34616305	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34730066	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35868882	0.85[AMR][1000 genomes]
rs3775836	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs399086	0.90[EUR][1000 genomes]
rs401950	0.90[EUR][1000 genomes]
rs428409	0.91[EUR][1000 genomes]
rs437027	0.91[EUR][1000 genomes]
rs439159	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4834698	0.96[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4834699	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7676832	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs960738	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs960739	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][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	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS 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	39 gene(s)	inside rSNPs	diseases
2	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv427693	chr4:119493919-119674742	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer 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	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119607200-119659200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:119607800-119693800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:119608600-119674000	Weak transcription	Stomach Mucosa	stomach
4	chr4:119620000-119660200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:119625800-119718000	Weak transcription	Hela-S3	cervix
6	chr4:119628000-119659800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:119630400-119674200	Weak transcription	A549	lung
8	chr4:119633200-119662800	Weak transcription	Brain Anterior Caudate	brain
9	chr4:119633400-119667600	Weak transcription	Brain Germinal Matrix	brain
10	chr4:119634400-119660000	Weak transcription	Brain Angular Gyrus	brain
11	chr4:119640600-119662200	Strong transcription	Fetal Muscle Trunk	muscle
12	chr4:119640800-119692600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr4:119641200-119659600	Strong transcription	Fetal Intestine Large	intestine
14	chr4:119641600-119659400	Strong transcription	Liver	Liver
15	chr4:119641600-119679800	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr4:119642000-119661200	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr4:119642000-119662000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr4:119642000-119662000	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr4:119642000-119666800	Strong transcription	Placenta	Placenta
20	chr4:119642200-119668200	Strong transcription	Duodenum Mucosa	Duodenum
21	chr4:119642400-119662000	Strong transcription	Adipose Nuclei	Adipose
22	chr4:119642400-119662000	Strong transcription	Fetal Lung	lung
23	chr4:119642400-119668400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr4:119643000-119662000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr4:119644200-119659600	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:119644400-119662000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:119644400-119662000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr4:119644400-119667400	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr4:119645400-119668200	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr4:119646200-119662200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:119646200-119667000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr4:119646600-119662000	Strong transcription	GM12878-XiMat	blood
33	chr4:119647400-119660400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr4:119649200-119659200	Weak transcription	Right Ventricle	heart
35	chr4:119649200-119665200	Weak transcription	Small Intestine	intestine
36	chr4:119649200-119666800	Weak transcription	Psoas Muscle	Psoas
37	chr4:119649200-119670600	Weak transcription	Brain Hippocampus Middle	brain
38	chr4:119649200-119675200	Weak transcription	Brain Substantia Nigra	brain
39	chr4:119649200-119687600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:119649200-119693600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr4:119649400-119659400	Weak transcription	Fetal Kidney	kidney
42	chr4:119649600-119664600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr4:119650600-119668400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr4:119651000-119659200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:119651400-119664600	Weak transcription	Fetal Brain Male	brain
46	chr4:119651800-119665400	Strong transcription	HUVEC	blood vessel
47	chr4:119651800-119672600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr4:119651800-119687400	Weak transcription	Thymus	Thymus
49	chr4:119652000-119658600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr4:119652000-119659000	Weak transcription	Primary B cells from peripheral blood	blood

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