Variant report

Variant	rs4540690
Chromosome Location	chr1:153825208-153825209
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10127484	0.81[EUR][1000 genomes]
rs10908512	0.81[EUR][1000 genomes]
rs10908525	0.85[EUR][1000 genomes]
rs10908526	0.85[EUR][1000 genomes]
rs11264573	0.85[EUR][1000 genomes]
rs11264621	0.80[EUR][1000 genomes]
rs1127091	0.87[EUR][1000 genomes]
rs1139620	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800001	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12120118	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124424	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129468	0.93[ASN][1000 genomes]
rs12130611	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133492	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133923	0.86[EUR][1000 genomes]
rs12142639	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12142733	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12738361	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252508	0.82[EUR][1000 genomes]
rs35711150	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4276953	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4341393	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4370789	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4451582	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4581307	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4596938	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61803655	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427300	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427306	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668066	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677794	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6690619	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6700115	0.86[EUR][1000 genomes]
rs72694233	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7414227	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7415004	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7522030	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7554469	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9426935	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9426938	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427232	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427233	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][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	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
4	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	nsv817392	chr1:153724807-153870005	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
7	esv1825076	chr1:153779296-153843413	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153781600-153826800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:153791800-153845600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:153800800-153825400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:153800800-153825400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:153800800-153825400	Weak transcription	Pancreas	Pancrea
6	chr1:153800800-153827000	Weak transcription	HUVEC	blood vessel
7	chr1:153800800-153830800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:153800800-153832600	Weak transcription	Aorta	Aorta
9	chr1:153800800-153832800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:153800800-153835600	Weak transcription	Ovary	ovary
11	chr1:153800800-153850800	Weak transcription	A549	lung
12	chr1:153800800-153852800	Weak transcription	Fetal Brain Female	brain
13	chr1:153800800-153852800	Weak transcription	Placenta	Placenta
14	chr1:153800800-153852800	Weak transcription	Left Ventricle	heart
15	chr1:153800800-153853000	Weak transcription	Fetal Kidney	kidney
16	chr1:153801200-153829800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:153801200-153829800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:153801600-153845800	Weak transcription	Lung	lung
19	chr1:153801800-153836600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:153806000-153827400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:153806200-153845400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:153814600-153827400	Weak transcription	Colonic Mucosa	Colon
23	chr1:153814800-153828400	Weak transcription	NHDF-Ad	bronchial
24	chr1:153814800-153835200	Weak transcription	Osteobl	bone
25	chr1:153814800-153839000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:153814800-153848000	Weak transcription	Fetal Heart	heart
27	chr1:153814800-153853400	Weak transcription	HSMMtube	muscle
28	chr1:153816000-153844000	Weak transcription	Right Ventricle	heart
29	chr1:153816600-153836200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:153816800-153834600	Weak transcription	Brain Angular Gyrus	brain
31	chr1:153818400-153825400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:153821200-153826000	Strong transcription	Fetal Intestine Small	intestine
33	chr1:153821400-153832800	Weak transcription	Gastric	stomach
34	chr1:153821600-153839800	Weak transcription	Small Intestine	intestine
35	chr1:153822000-153836000	Weak transcription	Liver	Liver
36	chr1:153822000-153838600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr1:153822400-153825400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:153822400-153826400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr1:153822600-153826000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:153822600-153826000	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr1:153822600-153839000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:153822600-153839400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:153822800-153853400	Weak transcription	HMEC	breast
44	chr1:153822800-153854200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:153823000-153826200	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr1:153823200-153826200	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr1:153823200-153826600	Strong transcription	Fetal Thymus	thymus
48	chr1:153823200-153833600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:153823400-153825800	Strong transcription	Duodenum Mucosa	Duodenum
50	chr1:153823400-153826000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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