Variant report

Variant	rs4290311
Chromosome Location	chr12:50229149-50229150
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50221596..50224125-chr12:50227777..50230858,4	MCF-7	breast:
2	chr12:50220112..50224669-chr12:50225407..50232096,10	K562	blood:
3	chr12:50225491..50228236-chr12:50228329..50230390,4	MCF-7	breast:
4	chr12:50222103..50225028-chr12:50228946..50232862,3	MCF-7	breast:
5	chr12:50226829..50229269-chr12:50234800..50236816,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258057	Chromatin interaction
ENSG00000167566	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10747567	0.83[EUR][1000 genomes]
rs10747568	0.83[EUR][1000 genomes]
rs10783321	0.84[EUR][1000 genomes]
rs10783323	0.83[EUR][1000 genomes]
rs10783326	0.82[EUR][1000 genomes]
rs10875984	0.82[EUR][1000 genomes]
rs11169167	0.96[ASN][1000 genomes]
rs1563168	0.81[EUR][1000 genomes]
rs1869504	0.86[EUR][1000 genomes]
rs2271687	0.82[EUR][1000 genomes]
rs2271688	0.82[EUR][1000 genomes]
rs3741557	0.82[EUR][1000 genomes]
rs3741558	0.81[EUR][1000 genomes]
rs4391887	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4898512	0.85[EUR][1000 genomes]
rs4898513	0.85[EUR][1000 genomes]
rs4898536	0.86[EUR][1000 genomes]
rs4898537	0.86[EUR][1000 genomes]
rs4898539	0.83[EUR][1000 genomes]
rs7137210	0.82[EUR][1000 genomes]
rs7295882	0.83[EUR][1000 genomes]
rs7302465	0.86[EUR][1000 genomes]
rs7306374	0.83[EUR][1000 genomes]
rs7307673	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7954572	0.83[EUR][1000 genomes]
rs7967564	0.84[EUR][1000 genomes]
rs7969178	0.83[EUR][1000 genomes]
rs7972100	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9805137	0.82[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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50222800-50235400	Weak transcription	Ovary	ovary
2	chr12:50222800-50236200	Weak transcription	Aorta	Aorta
3	chr12:50223000-50231800	Weak transcription	Pancreas	Pancrea
4	chr12:50223000-50232000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr12:50223000-50234600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:50223000-50234600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:50223000-50235000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:50223000-50235400	Weak transcription	Brain Anterior Caudate	brain
9	chr12:50223000-50235400	Weak transcription	Left Ventricle	heart
10	chr12:50223000-50235600	Weak transcription	Brain Substantia Nigra	brain
11	chr12:50223000-50236000	Weak transcription	Lung	lung
12	chr12:50223200-50231800	Weak transcription	Brain Hippocampus Middle	brain
13	chr12:50223200-50232000	Weak transcription	NHLF	lung
14	chr12:50223200-50235200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:50223200-50235200	Weak transcription	Liver	Liver
16	chr12:50223200-50235200	Weak transcription	HSMM	muscle
17	chr12:50223200-50235400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr12:50223200-50235400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:50223200-50235400	Weak transcription	Adipose Nuclei	Adipose
20	chr12:50223200-50235400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr12:50223200-50235400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:50223200-50235400	Weak transcription	Thymus	Thymus
23	chr12:50223200-50235400	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr12:50223200-50235400	Weak transcription	NHDF-Ad	bronchial
25	chr12:50223200-50235600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:50223400-50231800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:50223400-50231800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:50223400-50231800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr12:50223400-50232000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:50223400-50232000	Weak transcription	Fetal Muscle Leg	muscle
31	chr12:50223400-50232200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:50223400-50232600	Weak transcription	Fetal Thymus	thymus
33	chr12:50223400-50233200	Weak transcription	A549	lung
34	chr12:50223400-50234600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr12:50223400-50235000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:50223400-50235000	Weak transcription	Primary T cells from cord blood	blood
37	chr12:50223400-50235000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:50223400-50235000	Weak transcription	Hela-S3	cervix
39	chr12:50223400-50235200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr12:50223400-50235200	Weak transcription	Primary B cells from peripheral blood	blood
41	chr12:50223400-50235200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:50223400-50235200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:50223400-50235200	Weak transcription	Colon Smooth Muscle	Colon
44	chr12:50223400-50235200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:50223400-50235200	Weak transcription	Fetal Intestine Large	intestine
46	chr12:50223400-50235200	Weak transcription	Fetal Intestine Small	intestine
47	chr12:50223400-50235200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr12:50223400-50235400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr12:50223400-50235400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:50223400-50235400	Weak transcription	Fetal Lung	lung

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