Variant report

Variant	rs4958999
Chromosome Location	chr5:177377879-177377880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10060376	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10464066	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10464113	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10464116	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10794706	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11249783	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11738026	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11742117	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11742168	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11745692	0.80[ASN][1000 genomes]
rs12186510	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12187456	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13157329	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13157464	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13157845	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13167295	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13167457	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13167631	0.85[ASN][1000 genomes]
rs13172879	0.84[AFR][1000 genomes]
rs13190413	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4077204	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4077205	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4246052	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4318803	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4327608	0.84[ASN][1000 genomes]
rs4958944	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4958945	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958946	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958948	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958980	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4958982	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4958983	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4958992	0.85[ASN][1000 genomes]
rs4958995	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4958997	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4958998	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4959000	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4959001	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4959002	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4959003	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60355061	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62397830	0.95[ASN][1000 genomes]
rs62397831	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62397832	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6601187	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6861547	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6861572	0.84[AFR][1000 genomes]
rs6864280	0.81[ASN][1000 genomes]
rs6866295	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6875636	0.85[ASN][1000 genomes]
rs6880829	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6881018	0.83[ASN][1000 genomes]
rs6885392	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6896989	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs71591890	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs71591897	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7341034	0.81[AFR][1000 genomes]
rs7703493	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7705931	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7706237	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7706255	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7718261	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7730346	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7733233	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9764398	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9765519	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024444	chr5:176751921-177427715	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	142 gene(s)	inside rSNPs	diseases
2	esv2752795	chr5:176898619-177488281	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv1033211	chr5:177133646-177383386	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1030383	chr5:177310325-177571254	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv883184	chr5:177311043-177488281	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv883185	chr5:177357964-177401509	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv521629	chr5:177364884-177396200	Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv883186	chr5:177376317-177549491	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	esv20913	chr5:177376350-177379796	Strong transcription Weak transcription ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv883187	chr5:177377400-177419967	ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177366400-177378800	Weak transcription	Fetal Intestine Small	intestine
2	chr5:177368200-177396400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr5:177371000-177381800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:177371000-177393000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr5:177371600-177378800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr5:177371600-177383800	Weak transcription	Liver	Liver
7	chr5:177371600-177385200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:177371600-177389600	Weak transcription	Brain Germinal Matrix	brain
9	chr5:177371800-177378400	Weak transcription	Spleen	Spleen
10	chr5:177371800-177378600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:177371800-177378600	Weak transcription	NHLF	lung
12	chr5:177371800-177380600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr5:177371800-177384200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr5:177371800-177387400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr5:177371800-177387600	Weak transcription	Pancreas	Pancrea
16	chr5:177371800-177387800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:177371800-177388200	Weak transcription	Gastric	stomach
18	chr5:177371800-177390200	Weak transcription	Primary T cells from cord blood	blood
19	chr5:177371800-177390800	Weak transcription	Ovary	ovary
20	chr5:177371800-177392800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr5:177371800-177394200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr5:177371800-177394200	Weak transcription	Right Ventricle	heart
23	chr5:177372000-177381800	Weak transcription	Lung	lung
24	chr5:177372000-177382800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr5:177372000-177385200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr5:177372000-177385400	Weak transcription	NHDF-Ad	bronchial
27	chr5:177372200-177378400	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr5:177372200-177379400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:177372200-177390000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr5:177372400-177385600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr5:177372600-177385600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr5:177372600-177388200	Weak transcription	Esophagus	oesophagus
33	chr5:177374000-177378400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:177374200-177384400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr5:177374400-177385200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr5:177375200-177387600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:177375400-177385200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr5:177375400-177385200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr5:177375600-177381000	Weak transcription	Thymus	Thymus
40	chr5:177376800-177378600	Weak transcription	Fetal Stomach	stomach
41	chr5:177377200-177378000	Strong transcription	Primary B cells from peripheral blood	blood
42	chr5:177377200-177379200	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr5:177377400-177379200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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