Variant report

Variant	rs13010022
Chromosome Location	chr2:38909706-38909707
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38819202..38822030-chr2:38909046..38911240,2	K562	blood:
2	chr2:38823851..38826080-chr2:38908814..38911340,2	K562	blood:
3	chr2:38908524..38910141-chr2:38911332..38912843,2	MCF-7	breast:
4	chr2:38909532..38914838-chr2:38917160..38922190,4	K562	blood:
5	chr2:38903554..38905525-chr2:38909598..38912564,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10165289	0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs10186448	0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs12469458	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12469534	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12712612	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12987870	0.87[CEU][hapmap];0.85[GIH][hapmap]
rs13004674	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13004806	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13004842	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13005073	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13006376	0.85[CEU][hapmap];0.97[EUR][1000 genomes]
rs13011383	0.82[ASN][1000 genomes]
rs13012704	0.95[EUR][1000 genomes]
rs13016907	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13032255	0.84[ASN][1000 genomes]
rs13383762	1.00[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13399254	0.91[YRI][hapmap]
rs13421894	0.90[YRI][hapmap]
rs17023042	0.91[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs17576472	0.87[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17576507	0.87[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28716236	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34391548	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34533539	0.93[ASN][1000 genomes]
rs34558770	0.88[EUR][1000 genomes]
rs34756536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34875979	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34909144	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35448554	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35585199	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4670262	0.87[JPT][hapmap]
rs4670885	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58757994	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6707543	0.84[ASN][1000 genomes]
rs6736380	0.84[ASN][1000 genomes]
rs6741892	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873882	chr2:38858669-38921498	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv873883	chr2:38881106-38932777	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13010022	LAP3	trans	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38894000-38917600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr2:38894200-38919000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:38894400-38910400	Weak transcription	Psoas Muscle	Psoas
4	chr2:38894400-38917600	Weak transcription	NHDF-Ad	bronchial
5	chr2:38894400-38960600	Weak transcription	Brain Substantia Nigra	brain
6	chr2:38894600-38919600	Weak transcription	Fetal Heart	heart
7	chr2:38894800-38949400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:38895000-38917600	Weak transcription	HSMM	muscle
9	chr2:38895600-38912400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr2:38898600-38912400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:38898600-38921200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:38898800-38911600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr2:38901400-38917000	Weak transcription	HSMMtube	muscle
14	chr2:38902800-38916600	Strong transcription	Fetal Stomach	stomach
15	chr2:38903000-38909800	Strong transcription	Fetal Muscle Trunk	muscle
16	chr2:38903000-38912200	Strong transcription	Fetal Muscle Leg	muscle
17	chr2:38903000-38912400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:38903000-38912800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:38903200-38910400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:38903200-38910600	Strong transcription	Primary B cells from cord blood	blood
21	chr2:38903200-38912800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr2:38903400-38910600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:38903600-38923800	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:38903800-38918600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:38904400-38918400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr2:38904800-38936000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:38905000-38910400	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr2:38905000-38910600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr2:38905000-38911000	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr2:38905000-38911800	Weak transcription	Hela-S3	cervix
31	chr2:38905000-38913600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr2:38905000-38917000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:38905000-38917800	Weak transcription	Esophagus	oesophagus
34	chr2:38905000-38918400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr2:38905000-38935800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr2:38905000-38947600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:38905200-38912400	Weak transcription	Stomach Mucosa	stomach
38	chr2:38905200-38912400	Weak transcription	NHLF	lung
39	chr2:38905200-38912600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr2:38905200-38915400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr2:38905200-38920400	Strong transcription	Fetal Intestine Large	intestine
42	chr2:38905200-38925400	Weak transcription	Small Intestine	intestine
43	chr2:38905600-38911200	Strong transcription	Liver	Liver
44	chr2:38905600-38911400	Strong transcription	HepG2	liver
45	chr2:38905600-38917600	Strong transcription	Fetal Intestine Small	intestine
46	chr2:38906000-38911800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:38906400-38910000	Strong transcription	Left Ventricle	heart
48	chr2:38906400-38918800	Strong transcription	Duodenum Mucosa	Duodenum
49	chr2:38907800-38910000	Strong transcription	Rectal Smooth Muscle	rectum
50	chr2:38907800-38912200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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