Variant report

Variant	rs2913544
Chromosome Location	chr5:79377900-79377901
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10474605	0.86[EUR][1000 genomes]
rs1438735	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1438736	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1438737	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs166270	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2059794	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs2118731	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2241825	0.92[CEU][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2247450	0.94[ASW][hapmap];0.82[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2249687	0.92[CEU][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs2249794	0.86[EUR][1000 genomes]
rs2434277	0.90[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2434278	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2434280	0.81[EUR][1000 genomes]
rs2434282	0.81[EUR][1000 genomes]
rs2434299	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2434301	0.89[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2434302	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2434303	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2434304	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2434320	0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2438644	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2438645	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2438649	0.91[CEU][hapmap];0.81[CHB][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2451932	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs256442	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs256445	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2918422	0.91[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs364988	0.86[EUR][1000 genomes]
rs368287	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs368936	0.92[CEU][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs380747	0.95[CEU][hapmap];0.82[CHB][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs382746	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs384941	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs394947	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs397601	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs404375	0.92[CEU][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs405112	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs407314	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs411240	0.86[EUR][1000 genomes]
rs411943	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs412379	0.92[CEU][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs426623	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs428279	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs432267	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6861685	0.83[EUR][1000 genomes]
rs689879	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs690284	0.86[EUR][1000 genomes]
rs690325	0.84[EUR][1000 genomes]
rs692979	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs693270	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs7727310	0.86[JPT][hapmap]

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	nsv432748	chr5:79300434-79577760	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2913544	THBS4	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79351600-79379200	Weak transcription	Pancreas	Pancrea
2	chr5:79352400-79378200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr5:79354600-79378400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr5:79359600-79378200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr5:79360000-79378200	Weak transcription	Brain Angular Gyrus	brain
6	chr5:79361400-79378400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:79361600-79378400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr5:79361800-79378400	Strong transcription	Primary T cells from cord blood	blood
9	chr5:79362600-79378600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr5:79363000-79378800	Weak transcription	Thymus	Thymus
11	chr5:79364400-79378200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr5:79365800-79378200	Weak transcription	Fetal Stomach	stomach
13	chr5:79366000-79379000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr5:79366000-79388000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr5:79366200-79378200	Weak transcription	Adipose Nuclei	Adipose
16	chr5:79366200-79378400	Weak transcription	Fetal Intestine Small	intestine
17	chr5:79366200-79379000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr5:79366200-79385000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:79366200-79392400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:79366400-79378400	Weak transcription	Liver	Liver
21	chr5:79366400-79378600	Weak transcription	Placenta	Placenta
22	chr5:79366400-79379200	Weak transcription	Spleen	Spleen
23	chr5:79366600-79378200	Weak transcription	Fetal Thymus	thymus
24	chr5:79366600-79378400	Weak transcription	Fetal Kidney	kidney
25	chr5:79366600-79379000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr5:79366600-79379200	Weak transcription	Lung	lung
27	chr5:79366800-79379000	Weak transcription	Primary B cells from cord blood	blood
28	chr5:79369000-79378800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr5:79369200-79378600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr5:79369600-79378600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr5:79371000-79378200	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr5:79371000-79378400	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr5:79372800-79378200	Weak transcription	Esophagus	oesophagus
34	chr5:79372800-79378200	Weak transcription	Ovary	ovary
35	chr5:79373000-79378400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr5:79373200-79378600	Weak transcription	HSMMtube	muscle
37	chr5:79373200-79378800	Weak transcription	Left Ventricle	heart
38	chr5:79373400-79378600	Weak transcription	Right Atrium	heart
39	chr5:79373800-79378200	Weak transcription	Fetal Heart	heart
40	chr5:79373800-79378800	Weak transcription	Right Ventricle	heart
41	chr5:79374400-79378200	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr5:79374800-79381800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr5:79375000-79379200	Weak transcription	Gastric	stomach
44	chr5:79375600-79378400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr5:79375600-79378400	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr5:79375600-79378600	Weak transcription	K562	blood
47	chr5:79375800-79378200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:79375800-79378400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr5:79375800-79378400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr5:79376000-79378400	Weak transcription	Rectal Mucosa Donor 29	rectum

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