Variant report

Variant	rs4664587
Chromosome Location	chr2:153331400-153331401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10173899	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10179418	0.87[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap]
rs10180542	0.83[ASN][1000 genomes]
rs10193625	0.81[CEU][hapmap]
rs10194603	0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10208776	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10432493	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12616906	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12693378	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13390698	0.93[JPT][hapmap]
rs13424038	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13427076	0.94[JPT][hapmap]
rs13427990	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16831169	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs16831174	0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2068886	0.81[CEU][hapmap]
rs2078444	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2346205	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2346209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2881339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4143274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4146259	0.83[CEU][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs4664112	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4664589	0.82[ASN][1000 genomes]
rs4664590	0.82[ASN][1000 genomes]
rs58121347	0.84[ASN][1000 genomes]
rs59965317	0.93[ASN][1000 genomes]
rs6434059	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[ASN][1000 genomes]
rs6434060	0.94[ASN][1000 genomes]
rs6434061	0.97[ASN][1000 genomes]
rs6434062	0.94[ASN][1000 genomes]
rs6713348	0.80[ASN][1000 genomes]
rs6725661	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6737699	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs6747765	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6748954	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs73968029	0.86[ASN][1000 genomes]
rs7559217	0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7582984	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7586195	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7587794	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7590207	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7592283	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7606592	0.83[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[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	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv875291	chr2:153251742-153339823	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	esv2754362	chr2:153297577-153366129	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv875292	chr2:153308471-153357383	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv2830258	chr2:153318339-153349165	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153320800-153331600	Enhancers	Hela-S3	cervix
2	chr2:153324800-153340000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:153326000-153331600	Enhancers	Brain Cingulate Gyrus	brain
4	chr2:153326200-153332600	Weak transcription	Adipose Nuclei	Adipose
5	chr2:153326200-153333000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:153326200-153334200	Enhancers	Brain Anterior Caudate	brain
7	chr2:153326200-153339200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:153326200-153345800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:153327400-153331400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr2:153328000-153333200	Enhancers	Psoas Muscle	Psoas
11	chr2:153328200-153332400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:153328400-153332600	Weak transcription	Aorta	Aorta
13	chr2:153328600-153332400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:153328600-153334600	Enhancers	Brain Substantia Nigra	brain
15	chr2:153329000-153337200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:153329000-153337800	Weak transcription	Fetal Stomach	stomach
17	chr2:153329200-153331800	Enhancers	Brain Hippocampus Middle	brain
18	chr2:153329200-153340000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:153329400-153337600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:153329400-153338000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:153329600-153332400	Weak transcription	Brain Angular Gyrus	brain
22	chr2:153329600-153333600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:153329600-153337200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:153329600-153338200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:153329600-153338200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:153329600-153340000	Weak transcription	Ovary	ovary
27	chr2:153329800-153332200	Weak transcription	Left Ventricle	heart
28	chr2:153329800-153332400	Weak transcription	NHEK	skin
29	chr2:153330000-153332800	Weak transcription	Small Intestine	intestine
30	chr2:153330200-153331800	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr2:153330200-153337200	Weak transcription	Fetal Kidney	kidney
32	chr2:153330200-153339400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr2:153330400-153333600	Enhancers	A549	lung
34	chr2:153330400-153334000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:153330600-153332400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:153330600-153332600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:153330800-153332200	Weak transcription	Placenta	Placenta
38	chr2:153330800-153334000	Weak transcription	Liver	Liver
39	chr2:153330800-153334600	Enhancers	HepG2	liver
40	chr2:153330800-153336200	Weak transcription	Pancreas	Pancrea
41	chr2:153330800-153337200	Weak transcription	Fetal Lung	lung
42	chr2:153330800-153337200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr2:153330800-153342400	Weak transcription	Stomach Mucosa	stomach
44	chr2:153330800-153347400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:153331000-153332400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:153331200-153337800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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