Variant report

Variant	rs13144939
Chromosome Location	chr4:143288893-143288894
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1158692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1158693	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511267	0.83[AMR][1000 genomes]
rs13128245	0.83[AMR][1000 genomes]
rs13138212	0.85[CEU][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes]
rs1391098	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1489577	0.92[CEU][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.88[TSI][hapmap]
rs1489578	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs1497389	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap];0.93[AFR][1000 genomes]
rs1497397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1497398	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565306	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs17715707	1.00[ASW][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs1812174	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1814133	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982966	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[JPT][hapmap]
rs2029991	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173209	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2255497	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2627802	1.00[LWK][hapmap]
rs2627804	1.00[LWK][hapmap]
rs2627806	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2627837	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2635421	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2635422	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2635424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2635429	1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap]
rs2646085	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2646086	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2646087	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2646089	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2646090	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2646091	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs34830426	0.80[AMR][1000 genomes]
rs3775703	0.93[AFR][1000 genomes]
rs3775705	0.85[CEU][hapmap];0.80[JPT][hapmap]
rs3775716	1.00[YRI][hapmap]
rs3775718	1.00[ASW][hapmap];0.81[MKK][hapmap]
rs3775720	1.00[ASW][hapmap]
rs3822157	0.85[CEU][hapmap];0.80[JPT][hapmap]
rs6820232	1.00[YRI][hapmap]
rs6825345	0.80[AMR][1000 genomes]
rs716762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724131	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72724560	0.82[AMR][1000 genomes]
rs7699598	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs881611	0.92[CEU][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs882004	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882005	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931419	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs980808	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1027781	chr4:142943485-143306567	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830100	chr4:143216951-143393305	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13144939	LSM6	cis	cerebellum	SCAN
rs13144939	C4orf49	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143273400-143299000	Weak transcription	Left Ventricle	heart
2	chr4:143276200-143289800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr4:143277800-143289800	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr4:143278400-143294200	Weak transcription	Stomach Mucosa	stomach
5	chr4:143284800-143289400	Enhancers	HSMM	muscle
6	chr4:143285000-143294600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr4:143285200-143290200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:143285200-143298400	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr4:143285800-143289000	Weak transcription	Dnd41	blood
10	chr4:143285800-143289200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:143285800-143290000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:143285800-143290400	Enhancers	NHDF-Ad	bronchial
13	chr4:143286000-143289200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:143286000-143290600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:143286200-143289200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr4:143286200-143290000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr4:143286200-143290600	Enhancers	HMEC	breast
18	chr4:143286400-143290400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:143286800-143289000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:143286800-143293800	Weak transcription	Osteobl	bone
21	chr4:143287000-143293800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:143287600-143289000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr4:143287600-143289000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr4:143287600-143289200	Enhancers	Fetal Heart	heart
25	chr4:143287800-143289000	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr4:143288000-143289000	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr4:143288000-143289000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:143288000-143289000	Enhancers	Adipose Nuclei	Adipose
29	chr4:143288000-143289000	Enhancers	Stomach Smooth Muscle	stomach
30	chr4:143288000-143289200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr4:143288000-143290200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:143288000-143290200	Enhancers	HUVEC	blood vessel
33	chr4:143288000-143290400	Enhancers	Primary hematopoietic stem cells	blood
34	chr4:143288000-143290400	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr4:143288000-143290600	Enhancers	Primary T cells from cord blood	blood
36	chr4:143288000-143290600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr4:143288000-143293400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr4:143288200-143289000	Enhancers	H1 Cell Line	embryonic stem cell
39	chr4:143288200-143289000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr4:143288200-143289000	Weak transcription	Fetal Brain Female	brain
41	chr4:143288200-143289000	Enhancers	Right Atrium	heart
42	chr4:143288200-143289000	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr4:143288200-143289200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:143288200-143289200	Enhancers	Muscle Satellite Cultured Cells	--
45	chr4:143288200-143289200	Enhancers	NH-A	brain
46	chr4:143288200-143290000	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr4:143288400-143289000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr4:143288400-143289000	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr4:143288400-143290000	Weak transcription	HSMMtube	muscle
50	chr4:143288400-143293800	Weak transcription	Aorta	Aorta

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