Variant report

Variant	rs57585665
Chromosome Location	chr4:152327017-152327018
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152020743..152023351-chr4:152326497..152328231,2	MCF-7	breast:
2	chr4:152324300..152327192-chr4:152328168..152330030,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SH3D19-1	chr4:152326596-152330019	NONHSAT098755

Variant related genes	Relation type
ENSG00000251611	Chromatin interaction
ENSG00000201264	Chromatin interaction
ENSG00000145425	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10028035	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10454251	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11099811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11099815	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11099816	0.81[AMR][1000 genomes]
rs1143036	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729923	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11732918	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11733820	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11932398	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12647555	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1470280	0.80[EUR][1000 genomes]
rs1470281	0.80[EUR][1000 genomes]
rs1596290	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1899550	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2034061	0.81[AMR][1000 genomes]
rs2709812	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2709813	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2709814	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2709815	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2709816	0.84[AMR][1000 genomes]
rs2709817	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2709818	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2709819	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2709820	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2709821	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2709822	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2709823	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2709825	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2709826	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2709827	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2709828	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2709829	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2709831	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2709832	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2709833	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2709834	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2709838	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2709842	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2709844	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2724547	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2724550	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2724551	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2724553	0.88[EUR][1000 genomes]
rs2724555	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2724558	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2724563	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2724564	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2724565	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2724567	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2724568	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2724571	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2724574	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2724577	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2724578	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2724580	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28549769	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28622593	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28666858	0.82[AMR][1000 genomes]
rs4235219	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4254751	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4263379	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4266275	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4473638	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4519779	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4696088	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4696089	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4696092	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4696259	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4696260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696261	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59714108	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62327196	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6813735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843639	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6845648	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6851305	0.82[AFR][1000 genomes]
rs6851814	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6855845	0.80[AMR][1000 genomes]
rs73861275	0.82[AFR][1000 genomes]
rs7657670	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7657747	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7658169	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7676059	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7676922	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7677131	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7678823	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7680013	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7680236	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7682770	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7682837	0.81[AMR][1000 genomes]
rs7684462	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7691601	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7698816	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9968292	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9994482	0.84[AMR][1000 genomes];0.80[EUR][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	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1025192	chr4:152202627-152498890	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv537307	chr4:152202627-152498890	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv880624	chr4:152280646-152549112	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57585665	FAM160A1	cis	Whole Blood	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152316000-152328200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:152323600-152328400	Weak transcription	HepG2	liver
3	chr4:152324000-152328600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr4:152324000-152328800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:152324000-152329000	Weak transcription	Psoas Muscle	Psoas
6	chr4:152324000-152329000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:152324200-152328600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:152324400-152328000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr4:152324400-152328200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:152324400-152328800	Weak transcription	Fetal Intestine Large	intestine
11	chr4:152325200-152328000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:152325600-152328400	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr4:152325800-152328600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr4:152326800-152328400	Weak transcription	Gastric	stomach
15	chr4:152326800-152329000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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