Variant report

Variant	rs648538
Chromosome Location	chr13:30812309-30812310
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1099846	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1099848	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs169332	0.81[ASN][1000 genomes]
rs175730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1964165	0.88[EUR][1000 genomes]
rs202085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202094	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202095	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202096	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs202112	0.82[EUR][1000 genomes]
rs202113	0.90[EUR][1000 genomes]
rs202114	0.90[EUR][1000 genomes]
rs594411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs605095	0.81[ASN][1000 genomes]
rs652053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs666245	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs674253	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs846486	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs846488	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs861727	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832572	chr13:30650005-30835256	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats 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	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs648538	SLC46A3	cis	cerebellum	SCAN
rs648538	KATNAL1	Cis_1M	lymphoblastoid	RTeQTL
rs648538	KATNAL1	cis	lymphoblastoid	seeQTL
rs648538	N4BP2L1	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30774400-30812600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr13:30791000-30831400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr13:30796800-30831400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr13:30797000-30823400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr13:30797800-30814800	Weak transcription	Placenta	Placenta
6	chr13:30799200-30831400	Weak transcription	Aorta	Aorta
7	chr13:30799400-30812400	Weak transcription	Fetal Kidney	kidney
8	chr13:30799400-30814200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr13:30799400-30814400	Weak transcription	Brain Angular Gyrus	brain
10	chr13:30799400-30814400	Weak transcription	HepG2	liver
11	chr13:30799400-30823200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr13:30799400-30831600	Weak transcription	Right Ventricle	heart
13	chr13:30799600-30817400	Weak transcription	Brain Anterior Caudate	brain
14	chr13:30799600-30823400	Weak transcription	A549	lung
15	chr13:30799600-30823400	Weak transcription	NHEK	skin
16	chr13:30799600-30845200	Weak transcription	HMEC	breast
17	chr13:30801000-30821200	Weak transcription	Fetal Brain Male	brain
18	chr13:30801200-30815400	Weak transcription	Osteobl	bone
19	chr13:30801800-30815800	Weak transcription	Colon Smooth Muscle	Colon
20	chr13:30803000-30831400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr13:30803400-30827800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr13:30803600-30815000	Weak transcription	GM12878-XiMat	blood
23	chr13:30803600-30815400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr13:30803600-30830400	Weak transcription	Fetal Heart	heart
25	chr13:30803600-30831400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr13:30803800-30815800	Weak transcription	Fetal Intestine Small	intestine
27	chr13:30803800-30818000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr13:30803800-30823200	Weak transcription	Fetal Intestine Large	intestine
29	chr13:30804400-30831600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr13:30804800-30823400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr13:30805600-30814200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr13:30805600-30815000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr13:30805600-30815600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr13:30805600-30818800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr13:30805600-30822600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr13:30805600-30823200	Weak transcription	Liver	Liver
37	chr13:30805600-30823400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr13:30805600-30823400	Weak transcription	Fetal Brain Female	brain
39	chr13:30805600-30823400	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr13:30805600-30831600	Weak transcription	Left Ventricle	heart
41	chr13:30805600-30831600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr13:30805600-30841800	Weak transcription	Ovary	ovary
43	chr13:30805600-30853200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr13:30807600-30815000	Strong transcription	Primary B cells from cord blood	blood
45	chr13:30807800-30813200	Strong transcription	Primary hematopoietic stem cells	blood
46	chr13:30807800-30813200	Strong transcription	Dnd41	blood
47	chr13:30808200-30814800	Weak transcription	Psoas Muscle	Psoas
48	chr13:30808200-30823400	Weak transcription	Fetal Lung	lung
49	chr13:30808400-30812400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr13:30808800-30812800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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