Variant report

Variant	rs59089770
Chromosome Location	chr4:166182920-166182921
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11722307	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11722313	0.80[ASN][1000 genomes]
rs11723812	0.84[ASN][1000 genomes]
rs11725104	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11726821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729242	0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11730744	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11730816	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11733838	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009130	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28446212	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34274617	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34962116	0.80[ASN][1000 genomes]
rs35068327	0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs55951309	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56208210	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56229427	0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56246670	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56919208	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs57645545	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59229716	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs59263314	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs59639455	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs60197231	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60459687	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs60905916	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs72993964	0.80[ASN][1000 genomes]
rs72993975	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72995922	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72995990	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72995992	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72995999	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72997704	0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72997706	0.84[ASN][1000 genomes]
rs73860621	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73860622	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73860630	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs73875268	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv1021905	chr4:165852926-166212878	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv881168	chr4:165975122-166196438	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv980272	chr4:166179748-166197533	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:166129600-166196800	Weak transcription	Pancreas	Pancrea
2	chr4:166130600-166200800	Weak transcription	Lung	lung
3	chr4:166131600-166196800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:166132200-166193800	Weak transcription	Fetal Brain Female	brain
5	chr4:166137800-166194200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr4:166138400-166185600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:166144600-166218800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:166156200-166199200	Weak transcription	Ovary	ovary
9	chr4:166170000-166210000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:166170600-166209600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:166177000-166183000	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr4:166177000-166196000	Weak transcription	Gastric	stomach
13	chr4:166177200-166186800	Weak transcription	Fetal Kidney	kidney
14	chr4:166177200-166192000	Weak transcription	Brain Angular Gyrus	brain
15	chr4:166177200-166218800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:166177400-166183800	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr4:166177400-166185000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:166177400-166185000	Weak transcription	Fetal Intestine Small	intestine
19	chr4:166177400-166187000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr4:166177400-166199200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr4:166177400-166201200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr4:166177400-166201600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr4:166177400-166204200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:166177400-166209200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:166177400-166215200	Weak transcription	Fetal Stomach	stomach
26	chr4:166177400-166216000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr4:166177400-166218600	Weak transcription	Spleen	Spleen
28	chr4:166177400-166219000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr4:166177600-166183200	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr4:166177600-166194400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:166177800-166191800	Weak transcription	Primary B cells from peripheral blood	blood
32	chr4:166177800-166205000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:166178200-166194600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:166178400-166205600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr4:166178800-166185000	Weak transcription	Liver	Liver
36	chr4:166178800-166191800	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr4:166178800-166194600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr4:166178800-166197200	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr4:166178800-166200600	Weak transcription	Fetal Intestine Large	intestine
40	chr4:166178800-166207600	Weak transcription	Primary B cells from cord blood	blood
41	chr4:166178800-166209200	Weak transcription	Brain Substantia Nigra	brain
42	chr4:166178800-166209400	Weak transcription	Brain Anterior Caudate	brain
43	chr4:166178800-166218800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr4:166178800-166218800	Weak transcription	Esophagus	oesophagus
45	chr4:166180200-166194600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:166181200-166183600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr4:166181200-166183800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr4:166181200-166194200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr4:166181200-166199200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:166181200-166204600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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