Variant report

Variant	rs12505427
Chromosome Location	chr4:89927062-89927063
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10031518	0.82[ASN][1000 genomes]
rs10470936	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11722033	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11725475	0.86[ASN][1000 genomes]
rs11725938	0.81[ASN][1000 genomes]
rs11726708	0.82[ASN][1000 genomes]
rs12505696	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508371	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12508524	0.99[ASN][1000 genomes]
rs12509305	1.00[ASN][1000 genomes]
rs13129885	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13146548	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1398942	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs59684168	0.84[ASN][1000 genomes]
rs60770708	0.82[ASN][1000 genomes]
rs61315828	0.84[ASN][1000 genomes]
rs67850063	0.95[ASN][1000 genomes]
rs6838424	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7691363	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9307058	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9790655	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv998651	chr4:89800245-89933445	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv537175	chr4:89800245-89933445	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv461577	chr4:89904124-89986326	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv594807	chr4:89904124-89986326	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89878400-89927600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:89896800-89934800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr4:89903000-89957200	Weak transcription	HSMM	muscle
4	chr4:89903400-89936000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:89904200-89927600	Weak transcription	Pancreas	Pancrea
6	chr4:89906600-89927400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:89907800-89927400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr4:89908800-89927400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr4:89909800-89931200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr4:89910400-89927600	Weak transcription	Ovary	ovary
11	chr4:89911400-89930400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr4:89912200-89935800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:89912200-89943800	Weak transcription	Psoas Muscle	Psoas
14	chr4:89912400-89927600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr4:89913400-89930800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:89913400-89944000	Weak transcription	Gastric	stomach
17	chr4:89915800-89927200	Weak transcription	Fetal Muscle Leg	muscle
18	chr4:89917200-89927400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr4:89920000-89927200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:89920400-89937000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr4:89921000-89930000	Weak transcription	Liver	Liver
22	chr4:89921000-89950600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr4:89922000-89927600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr4:89922400-89936000	Weak transcription	Adipose Nuclei	Adipose
25	chr4:89922600-89927600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:89922600-89932600	Weak transcription	NHDF-Ad	bronchial
27	chr4:89922600-89935000	Weak transcription	Placenta	Placenta
28	chr4:89922600-89936800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:89922600-89949800	Weak transcription	HMEC	breast
30	chr4:89922800-89927600	Weak transcription	HepG2	liver
31	chr4:89922800-89931800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:89922800-89935800	Weak transcription	HUVEC	blood vessel
33	chr4:89922800-89945600	Weak transcription	A549	lung
34	chr4:89923000-89927400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:89923000-89932200	Weak transcription	Osteobl	bone
36	chr4:89923000-89935000	Weak transcription	Fetal Kidney	kidney
37	chr4:89923400-89939400	Weak transcription	Primary T cells from cord blood	blood
38	chr4:89923600-89927600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:89923600-89927600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr4:89923600-89930800	Weak transcription	Small Intestine	intestine
41	chr4:89923600-89945600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr4:89923800-89927200	Weak transcription	Fetal Intestine Small	intestine
43	chr4:89923800-89927400	Weak transcription	Fetal Intestine Large	intestine
44	chr4:89923800-89927400	Weak transcription	Fetal Stomach	stomach
45	chr4:89923800-89927400	Weak transcription	K562	blood
46	chr4:89923800-89927600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr4:89923800-89928800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr4:89923800-89930400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr4:89923800-89936000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr4:89923800-89936000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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