Variant report

Variant	rs13138280
Chromosome Location	chr4:90046848-90046849
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:90033016..90036136-chr4:90045912..90049753,4	K562	blood:

Variant related genes	Relation type
ENSG00000180346	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10033484	0.86[JPT][hapmap];0.86[MEX][hapmap]
rs11737182	0.90[ASW][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs1398940	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs1458557	0.86[JPT][hapmap];0.86[MEX][hapmap]
rs16996143	0.86[JPT][hapmap]
rs16996144	0.80[GIH][hapmap]
rs17015027	0.86[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs17015052	0.91[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs1708668	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs1708669	0.91[JPT][hapmap]
rs1708670	0.89[ASW][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs1795722	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs1795727	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs1795734	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs1795738	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs1903007	0.86[JPT][hapmap]
rs1921679	0.82[JPT][hapmap];0.86[MEX][hapmap]
rs1921681	0.80[GIH][hapmap]
rs1921684	0.86[JPT][hapmap]
rs1961979	0.86[JPT][hapmap]
rs2018779	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2037036	0.81[TSI][hapmap]
rs2085601	0.86[JPT][hapmap]
rs2178583	0.86[JPT][hapmap]
rs2178584	0.86[JPT][hapmap];0.86[MEX][hapmap]
rs2178585	0.86[JPT][hapmap]
rs2609275	0.86[JPT][hapmap]
rs2670623	0.83[JPT][hapmap]
rs2704571	0.90[JPT][hapmap]
rs2704573	0.86[JPT][hapmap]
rs2704577	0.86[JPT][hapmap]
rs2869971	0.86[JPT][hapmap]
rs2869972	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2904261	0.89[ASW][hapmap];0.86[JPT][hapmap]
rs34845187	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35624987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4285052	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4507326	0.86[JPT][hapmap]
rs4555592	0.84[JPT][hapmap]
rs4642211	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59924504	0.83[AFR][1000 genomes]
rs60618725	0.93[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62306364	0.84[AMR][1000 genomes]
rs62306391	0.93[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62306397	0.83[AFR][1000 genomes]
rs6821678	0.90[ASW][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6844655	0.86[JPT][hapmap]
rs6852373	0.91[JPT][hapmap]
rs6853480	0.86[JPT][hapmap]
rs72877642	0.93[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7686954	0.82[ASW][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs7697075	0.86[JPT][hapmap]
rs7697900	0.90[ASW][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs9307054	0.86[JPT][hapmap]
rs9307055	0.81[JPT][hapmap]
rs9307061	0.86[JPT][hapmap]
rs9991237	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13138280	FAM190A	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90033400-90048200	Weak transcription	Ovary	ovary
2	chr4:90033400-90049200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:90033600-90049200	Weak transcription	Gastric	stomach
4	chr4:90033600-90052200	Weak transcription	Aorta	Aorta
5	chr4:90034800-90049200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:90042200-90047600	Enhancers	Fetal Intestine Large	intestine
7	chr4:90042600-90049600	Enhancers	Fetal Intestine Small	intestine
8	chr4:90043400-90050200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:90044800-90056000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:90045000-90047000	Weak transcription	Brain Substantia Nigra	brain
11	chr4:90045200-90047200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:90045800-90047200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:90045800-90047400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:90045800-90047400	Weak transcription	HepG2	liver
15	chr4:90045800-90047800	Enhancers	A549	lung
16	chr4:90046000-90056200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:90046600-90047800	Enhancers	Liver	Liver
18	chr4:90046800-90047400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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