Variant report

Variant	rs2412530
Chromosome Location	chr15:40841486-40841487
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40839583..40841943-chr15:40885345..40887458,2	K562	blood:

Variant related genes	Relation type
ENSG00000137812	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10444792	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10518696	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10851397	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11070276	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11070278	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11632319	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11637275	0.83[AFR][1000 genomes]
rs12442697	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12916218	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1453182	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1530942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1530943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16970734	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16970854	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1801320	1.00[CEU][hapmap]
rs1869303	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1987795	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2014367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2034653	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2084941	0.83[EUR][1000 genomes]
rs2278887	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2278889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2304579	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs2412528	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2412533	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2924389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2959547	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3803354	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4467046	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4561439	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4923873	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4923877	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4923878	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4923879	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4924473	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4924474	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4924476	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4924482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4924483	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57140606	0.90[EUR][1000 genomes]
rs57736474	0.89[EUR][1000 genomes]
rs582736	0.87[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs589650	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs607118	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs611933	0.87[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs617031	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs623187	1.00[CEU][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs624486	0.87[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs640919	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6492952	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6492953	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6492955	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs651131	0.82[EUR][1000 genomes]
rs667623	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7163648	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7163889	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7164056	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7164166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7164405	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7167239	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7167922	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7168913	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7168927	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7170073	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7170327	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7170946	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73396510	0.89[EUR][1000 genomes]
rs73396515	0.89[EUR][1000 genomes]
rs8024579	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8024802	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8029208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8032453	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033739	0.98[EUR][1000 genomes]
rs8034726	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8038350	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8040187	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8041816	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8041991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043197	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs896797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9284288	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs976402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9783737	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

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	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
3	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2412530	C15orf57	cis	Whole Blood	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40816800-40845600	Weak transcription	Ovary	ovary
2	chr15:40819600-40845000	Weak transcription	Pancreas	Pancrea
3	chr15:40821400-40848000	Weak transcription	Brain Anterior Caudate	brain
4	chr15:40821800-40856400	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:40822600-40856400	Weak transcription	Small Intestine	intestine
6	chr15:40823800-40841800	Weak transcription	Brain Substantia Nigra	brain
7	chr15:40824800-40842600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr15:40827600-40842000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr15:40828000-40856600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr15:40828600-40841600	Weak transcription	Colonic Mucosa	Colon
11	chr15:40829200-40845200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr15:40829400-40845000	Weak transcription	NHLF	lung
13	chr15:40829600-40845000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:40829600-40845200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:40829800-40845400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr15:40829800-40846000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:40831600-40856600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:40831800-40843600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr15:40831800-40845800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr15:40832000-40844800	Weak transcription	Aorta	Aorta
21	chr15:40832000-40845600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:40832000-40845800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:40832600-40845200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:40833400-40845200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:40834600-40845200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr15:40834800-40842200	Weak transcription	K562	blood
27	chr15:40837600-40842600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr15:40837800-40841800	Weak transcription	Dnd41	blood
29	chr15:40837800-40845200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:40838000-40845200	Genic enhancers	Primary B cells from peripheral blood	blood
31	chr15:40838000-40848200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr15:40838000-40856400	Weak transcription	A549	lung
33	chr15:40838200-40845800	Weak transcription	Brain Germinal Matrix	brain
34	chr15:40838200-40846600	Strong transcription	Fetal Intestine Small	intestine
35	chr15:40838600-40841600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr15:40838600-40847000	Weak transcription	Fetal Brain Male	brain
37	chr15:40838600-40852800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr15:40838600-40855600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr15:40838800-40846200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr15:40838800-40846600	Strong transcription	Fetal Stomach	stomach
41	chr15:40839000-40841600	Strong transcription	Placenta	Placenta
42	chr15:40839000-40841600	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr15:40839000-40845800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr15:40839000-40847200	Weak transcription	Brain Angular Gyrus	brain
45	chr15:40839200-40841800	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr15:40839200-40842000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr15:40839200-40842400	Enhancers	Psoas Muscle	Psoas
48	chr15:40839200-40842600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:40839200-40843000	Strong transcription	Esophagus	oesophagus
50	chr15:40839200-40843200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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