Variant report

Variant	rs1497389
Chromosome Location	chr4:143304592-143304593
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1158692	0.85[CEU][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap]
rs11722756	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11728236	1.00[YRI][hapmap]
rs12511267	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13128245	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13135641	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13138212	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13140802	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13144939	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]
rs1391098	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs1489577	0.92[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1489578	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1497397	0.84[CEU][hapmap];0.81[JPT][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap]
rs1497398	0.84[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1565306	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17715707	1.00[ASW][hapmap];0.80[MKK][hapmap]
rs1812174	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs1982966	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2029991	0.81[AMR][1000 genomes]
rs2173209	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306913	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2627802	1.00[LWK][hapmap]
rs2627804	1.00[LWK][hapmap]
rs2635424	0.85[CEU][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs2635429	1.00[LWK][hapmap]
rs2646085	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs2646091	0.90[JPT][hapmap]
rs34830426	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35151914	0.85[ASN][1000 genomes]
rs3775703	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3775705	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3775706	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3775710	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3775711	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3775718	1.00[ASW][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs3775720	1.00[ASW][hapmap]
rs3822157	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs6825345	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs716762	0.85[CEU][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs724131	0.85[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs72724560	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7699598	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs881611	0.92[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs931419	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs983767	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1497389	LSM6	cis	cerebellum	SCAN
rs1497389	NDUFC1	cis	parietal	SCAN
rs1497389	GYPB	cis	parietal	SCAN
rs1497389	C4orf49	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143290400-143305800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:143290400-143322000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr4:143294200-143305400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:143295200-143305000	Weak transcription	Small Intestine	intestine
5	chr4:143296600-143310200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr4:143299800-143304600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr4:143300200-143326200	Weak transcription	Aorta	Aorta
8	chr4:143300600-143304600	Weak transcription	Primary T cells from cord blood	blood
9	chr4:143301200-143308600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr4:143301200-143326200	Weak transcription	Gastric	stomach
11	chr4:143301400-143308000	Weak transcription	Fetal Muscle Leg	muscle
12	chr4:143301400-143316200	Weak transcription	Dnd41	blood
13	chr4:143301600-143304600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr4:143301600-143304800	Weak transcription	Placenta	Placenta
15	chr4:143301600-143305000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:143301600-143306000	Weak transcription	Right Ventricle	heart
17	chr4:143301600-143308000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr4:143301600-143308200	Weak transcription	Osteobl	bone
19	chr4:143301600-143312400	Weak transcription	Psoas Muscle	Psoas
20	chr4:143301600-143317400	Weak transcription	NH-A	brain
21	chr4:143301600-143322800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:143301600-143323200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:143301600-143325400	Weak transcription	Left Ventricle	heart
24	chr4:143301800-143304800	Weak transcription	HSMMtube	muscle
25	chr4:143301800-143309600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr4:143302200-143304600	Weak transcription	NHDF-Ad	bronchial
27	chr4:143302200-143315000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:143302200-143316400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr4:143302200-143323000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:143302400-143304600	Weak transcription	Fetal Heart	heart
31	chr4:143302400-143304600	Weak transcription	NHLF	lung
32	chr4:143302400-143305200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
33	chr4:143302400-143305600	Weak transcription	A549	lung
34	chr4:143303000-143304600	Weak transcription	NHEK	skin
35	chr4:143303600-143304600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:143303600-143305000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:143304000-143304800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:143304200-143305400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr4:143304200-143305600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr4:143304200-143305800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:143304200-143306400	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr4:143304400-143304600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr4:143304400-143305200	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr4:143304400-143305400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr4:143304400-143305400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr4:143304400-143305600	Enhancers	Muscle Satellite Cultured Cells	--
47	chr4:143304400-143305600	Genic enhancers	HSMM	muscle
48	chr4:143304400-143305800	Enhancers	HMEC	breast
49	chr4:143304400-143306200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
50	chr4:143304400-143307800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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