Variant report

Variant	rs4924474
Chromosome Location	chr15:40802247-40802248
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40800544..40802364-chr15:40805331..40807319,2	MCF-7	breast:
2	chr15:40761396..40764374-chr15:40800140..40802676,2	K562	blood:
3	chr15:40800305..40802269-chr15:40802285..40805070,2	K562	blood:
4	chr15:40730812..40737363-chr15:40801226..40806622,9	K562	blood:
5	chr15:40801534..40804191-chr15:40830855..40832642,2	K562	blood:

Variant related genes	Relation type
ENSG00000140320	Chromatin interaction
ENSG00000169105	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10444792	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10518696	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10851397	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11070276	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070278	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11632319	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12442697	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12916218	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1530942	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1530943	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16970734	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16970854	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1869303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1987795	0.91[AMR][1000 genomes]
rs2014367	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2034653	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2084941	0.85[EUR][1000 genomes]
rs2278889	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2290379	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2412528	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2412530	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2412533	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2924389	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2959535	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2959547	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3803354	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4467046	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4561439	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4923873	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4923877	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4923878	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4923879	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4924473	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924476	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4924482	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4924483	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57140606	0.89[EUR][1000 genomes]
rs57736474	0.87[EUR][1000 genomes]
rs582736	0.86[EUR][1000 genomes]
rs589650	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs607118	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs611933	0.86[EUR][1000 genomes]
rs617031	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs623187	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs624486	0.88[EUR][1000 genomes]
rs640919	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6492952	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6492953	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6492955	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs651131	0.84[EUR][1000 genomes]
rs667623	0.83[EUR][1000 genomes]
rs7163648	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7163889	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7164056	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7164166	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7164405	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7167239	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7167922	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7168913	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7168927	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7169872	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7170073	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7170327	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7170946	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73396510	0.87[EUR][1000 genomes]
rs73396515	0.87[EUR][1000 genomes]
rs8024579	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8024802	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8029208	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8032453	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8033739	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034726	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8038350	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8040187	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8041816	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8041991	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8043197	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs896797	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs921624	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9284288	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs976402	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9783737	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4924474	C15orf57	cis	Whole Blood	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40799200-40803200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:40799600-40802800	Weak transcription	Spleen	Spleen
3	chr15:40799800-40802400	Weak transcription	Right Ventricle	heart
4	chr15:40799800-40802600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr15:40799800-40802600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr15:40799800-40802800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:40799800-40802800	Weak transcription	Liver	Liver
8	chr15:40799800-40802800	Weak transcription	Brain Anterior Caudate	brain
9	chr15:40799800-40802800	Weak transcription	Brain Hippocampus Middle	brain
10	chr15:40799800-40802800	Weak transcription	Left Ventricle	heart
11	chr15:40799800-40802800	Weak transcription	Psoas Muscle	Psoas
12	chr15:40799800-40803000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:40799800-40803000	Weak transcription	Ovary	ovary
14	chr15:40799800-40803000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr15:40799800-40803200	Weak transcription	Brain Substantia Nigra	brain
16	chr15:40799800-40803200	Weak transcription	Colon Smooth Muscle	Colon
17	chr15:40799800-40803200	Weak transcription	Pancreas	Pancrea
18	chr15:40799800-40803200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr15:40799800-40803200	Weak transcription	HMEC	breast
20	chr15:40799800-40803400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:40799800-40803400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:40799800-40803400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:40799800-40803400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr15:40799800-40803400	Weak transcription	Right Atrium	heart
25	chr15:40800000-40802800	Weak transcription	K562	blood
26	chr15:40800000-40803600	Weak transcription	A549	lung
27	chr15:40801000-40803400	Enhancers	Placenta	Placenta

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