Variant report

Variant	rs2587024
Chromosome Location	chr3:146251433-146251434
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:146219569..146222344-chr3:146250325..146252358,2	K562	blood:
2	chr3:146250212..146252828-chr3:146254951..146257363,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1057481	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1079369	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13064509	1.00[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13069082	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1373246	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1443827	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs16858420	0.94[JPT][hapmap];0.81[YRI][hapmap]
rs1882971	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1882972	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1882973	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1882974	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1997601	0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1997604	0.82[ASW][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.98[ASN][1000 genomes]
rs2120381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.87[JPT][hapmap];0.90[LWK][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2165948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587007	0.98[ASN][1000 genomes]
rs2587008	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2587009	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2587010	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587011	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587012	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587013	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587014	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587016	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587017	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587018	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587021	0.95[CEU][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2587023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609858	0.91[ASN][1000 genomes]
rs2609860	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2609861	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2609862	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609864	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609865	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609866	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609867	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2688688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2738905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2738906	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2738907	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2738910	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2738911	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2738912	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2738915	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2738916	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2738918	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2738920	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2738923	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35214899	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3773510	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3773521	0.86[CHB][hapmap]
rs67703040	0.83[ASN][1000 genomes]
rs7615988	0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs9289722	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs977758	0.85[ASN][1000 genomes]
rs9815834	0.86[CHB][hapmap]
rs9861142	0.92[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs9865918	0.87[ASN][1000 genomes]
rs9876886	1.00[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9880682	0.86[CHB][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	esv3448053	chr3:146186791-146262066	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv3523751	chr3:146186838-146261806	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv3523753	chr3:146186838-146261806	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv2496437	chr3:146186902-146262961	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2587024	PLSCR1	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146224800-146254400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr3:146225400-146255000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:146225400-146256600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:146225400-146257000	Weak transcription	Right Ventricle	heart
5	chr3:146225400-146260800	Weak transcription	NH-A	brain
6	chr3:146225600-146252200	Weak transcription	Psoas Muscle	Psoas
7	chr3:146225600-146258600	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:146229000-146253200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr3:146229000-146259600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:146229400-146252200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr3:146229800-146257000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:146231600-146254400	Weak transcription	Brain Anterior Caudate	brain
13	chr3:146231600-146254400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:146231600-146257200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr3:146231600-146258600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr3:146231600-146259000	Weak transcription	Brain Angular Gyrus	brain
17	chr3:146231600-146260800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:146231800-146254000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:146231800-146254400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:146232000-146257400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr3:146232000-146259600	Weak transcription	NHDF-Ad	bronchial
22	chr3:146232800-146254400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:146232800-146256000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:146233000-146255200	Weak transcription	Esophagus	oesophagus
25	chr3:146233000-146259800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:146233000-146261400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr3:146233600-146259200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:146234400-146258000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:146235800-146251600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:146236200-146254400	Weak transcription	Gastric	stomach
31	chr3:146236200-146254600	Weak transcription	Spleen	Spleen
32	chr3:146237000-146253200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:146237000-146254400	Weak transcription	Brain Substantia Nigra	brain
34	chr3:146237200-146252200	Strong transcription	Dnd41	blood
35	chr3:146237200-146253000	Strong transcription	Fetal Thymus	thymus
36	chr3:146237200-146253400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr3:146237400-146254400	Weak transcription	Stomach Mucosa	stomach
38	chr3:146240000-146254600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr3:146240400-146257200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr3:146240800-146254400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:146241400-146254400	Weak transcription	Small Intestine	intestine
42	chr3:146241800-146255000	Weak transcription	Lung	lung
43	chr3:146241800-146258600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr3:146243000-146253200	Strong transcription	Fetal Intestine Large	intestine
45	chr3:146244200-146252800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:146244600-146252000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:146244800-146254600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:146244800-146258200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr3:146245200-146252000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr3:146245400-146252000	Strong transcription	Hela-S3	cervix

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