Variant report

Variant	rs4239580
Chromosome Location	chr19:35670208-35670209
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:35656275..35658757-chr19:35668459..35673698,5	K562	blood:
2	chr19:35659165..35661294-chr19:35670153..35671780,2	K562	blood:
3	chr19:35669103..35671214-chr19:35737457..35739938,2	K562	blood:

Variant related genes	Relation type
ENSG00000105699	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10401279	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10401570	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10401602	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10401634	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10402137	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10403511	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10404280	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10409862	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10409866	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10411557	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10412664	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10414022	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10415414	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10415832	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10416092	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10416492	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10419422	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10419636	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10419663	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10420111	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10423443	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10423916	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10424306	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10424450	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10424585	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10424799	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10425525	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10425753	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10426076	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10426303	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10426624	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10426966	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11084805	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11084806	0.89[EUR][1000 genomes]
rs11882781	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12052106	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12052192	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12052194	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12459615	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12460093	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12609714	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12610364	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12972110	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12974228	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12974983	0.86[AMR][1000 genomes]
rs2008052	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28413711	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34413985	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34677175	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34998055	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35921432	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4416138	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4805111	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4805112	0.87[EUR][1000 genomes]
rs4805113	0.86[EUR][1000 genomes]
rs4805114	0.85[EUR][1000 genomes]
rs4806099	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4806100	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4806101	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4806102	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4806103	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4806104	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4806105	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4806106	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4806107	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4806110	0.87[EUR][1000 genomes]
rs56413999	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58300983	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61192962	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7247878	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8102182	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8102391	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8102410	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8103035	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8103326	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8104301	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8106308	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8108988	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8109212	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8112633	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9304868	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9304869	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[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	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	esv2757694	chr19:35653642-35673333	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv2758757	chr19:35653642-35673333	Genic enhancers Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv2470	chr19:35655281-35702565	Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
6	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
7	nsv516540	chr19:35660450-35685536	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv817831	chr19:35661787-35673243	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv579368	chr19:35661787-35680002	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv579377	chr19:35662257-35673243	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4239580	FXYD5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35660800-35673400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr19:35661800-35673400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:35664200-35670400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:35665200-35670400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr19:35667400-35670800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:35668400-35671000	Enhancers	Placenta	Placenta
7	chr19:35668800-35670800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr19:35669000-35670400	Weak transcription	K562	blood
9	chr19:35669200-35670400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr19:35669600-35670400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr19:35669600-35671600	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr19:35669800-35670400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr19:35669800-35672000	Enhancers	Primary T cells from cord blood	blood
14	chr19:35669800-35672200	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr19:35669800-35672400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr19:35669800-35672400	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr19:35670000-35671800	Enhancers	Primary T cells fromperipheralblood	blood
18	chr19:35670000-35671800	Enhancers	Fetal Thymus	thymus
19	chr19:35670200-35670600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr19:35670200-35671000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:35670200-35671000	Weak transcription	Thymus	Thymus
22	chr19:35670200-35671800	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr19:35670200-35671800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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