Variant report

Variant	rs12500228
Chromosome Location	chr4:107041879-107041880
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:107023929..107026888-chr4:107039825..107042203,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10002288	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10084928	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11725065	0.83[AMR][1000 genomes]
rs11735326	1.00[CHD][hapmap]
rs12500331	0.86[AMR][1000 genomes]
rs12506205	1.00[CHD][hapmap]
rs12507874	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12508552	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12643397	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13534	0.85[AMR][1000 genomes]
rs28507027	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28697941	0.98[MKK][hapmap]
rs28765420	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28787305	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28814088	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28866820	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28868894	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28875879	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4323181	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4337798	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4339284	0.82[AMR][1000 genomes]
rs4521418	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4597909	1.00[CHD][hapmap]
rs6810877	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6816614	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6829795	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6835216	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6844324	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7657975	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7658011	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7658701	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7662806	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7662836	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7664188	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7669087	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7671145	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7674381	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7674466	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7698386	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799793	chr4:107000462-107062671	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv1801716	chr4:107000462-107062671	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv1849248	chr4:107000462-107062671	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv1850577	chr4:107000462-107062671	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv511247	chr4:107022702-107065220	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv879701	chr4:107024776-107163128	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv4450	chr4:107037823-107082669	Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12500228	SCYE1	Cis_1M	lymphoblastoid	RTeQTL
rs12500228	MGC16169	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:107031600-107052600	Weak transcription	Fetal Thymus	thymus
2	chr4:107031800-107053400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:107032000-107052200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:107032000-107058200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:107033400-107053000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr4:107033600-107052800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:107033600-107053400	Weak transcription	Osteobl	bone
8	chr4:107033800-107053400	Weak transcription	HSMM	muscle
9	chr4:107034200-107053400	Weak transcription	Right Ventricle	heart
10	chr4:107035200-107057200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:107035600-107083200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:107035800-107043800	Weak transcription	Thymus	Thymus
13	chr4:107035800-107052200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr4:107035800-107053000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr4:107035800-107053000	Weak transcription	Fetal Lung	lung
16	chr4:107035800-107053200	Weak transcription	Fetal Stomach	stomach
17	chr4:107035800-107053200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr4:107035800-107053400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:107035800-107053400	Weak transcription	Lung	lung
20	chr4:107035800-107053400	Weak transcription	Pancreas	Pancrea
21	chr4:107035800-107053600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:107035800-107053600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr4:107036000-107053200	Weak transcription	Brain Anterior Caudate	brain
24	chr4:107036200-107052800	Weak transcription	Fetal Muscle Leg	muscle
25	chr4:107037200-107053000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:107037400-107053400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr4:107037400-107053400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr4:107037600-107047000	Weak transcription	GM12878-XiMat	blood
29	chr4:107037600-107053400	Weak transcription	Brain Hippocampus Middle	brain
30	chr4:107037600-107056200	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr4:107037600-107060600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr4:107037600-107061600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:107037600-107066400	Weak transcription	Fetal Kidney	kidney
34	chr4:107037800-107053000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr4:107037800-107053000	Weak transcription	Liver	Liver
36	chr4:107037800-107053400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr4:107037800-107053400	Weak transcription	Adipose Nuclei	Adipose
38	chr4:107037800-107053400	Weak transcription	HepG2	liver
39	chr4:107037800-107077400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:107038000-107047200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr4:107038000-107052400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:107038000-107052800	Weak transcription	Brain Substantia Nigra	brain
43	chr4:107038000-107053000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr4:107038000-107053000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr4:107038000-107053200	Weak transcription	Primary B cells from cord blood	blood
46	chr4:107038000-107053400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr4:107038000-107053400	Weak transcription	Aorta	Aorta
48	chr4:107038000-107053400	Weak transcription	Left Ventricle	heart
49	chr4:107038000-107053400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr4:107038000-107055400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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