Variant report

Variant	rs1497397
Chromosome Location	chr4:143281873-143281874
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:143277710..143279872-chr4:143280001..143282986,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1158692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1158693	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511267	0.83[AMR][1000 genomes]
rs13128245	0.83[AMR][1000 genomes]
rs13138212	1.00[ASW][hapmap];0.84[CEU][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs13144939	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]
rs1391098	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1489577	0.92[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap]
rs1489578	0.92[CEU][hapmap];0.91[GIH][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap]
rs1497389	0.84[CEU][hapmap];0.81[JPT][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap]
rs1497398	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565306	0.84[AMR][1000 genomes]
rs1812174	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1814133	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982966	0.84[CEU][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap]
rs2029991	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173209	0.82[AMR][1000 genomes]
rs2255497	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2627806	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2627837	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2635421	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2635422	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2635424	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2646085	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2646086	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2646087	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2646089	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2646090	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2646091	0.90[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs34830426	0.80[AMR][1000 genomes]
rs3775705	0.84[CEU][hapmap]
rs3822157	0.84[CEU][hapmap]
rs6825345	0.80[AMR][1000 genomes]
rs716762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724131	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72724560	0.82[AMR][1000 genomes]
rs7699598	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs881611	0.92[CEU][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs882004	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882005	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931419	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs980808	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	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	nsv830099	chr4:143138257-143285055	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	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
rs1497397	LSM6	cis	cerebellum	SCAN
rs1497397	C4orf49	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143268400-143283200	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr4:143270800-143284000	Enhancers	Primary T killer memory cells from peripheral blood	blood
3	chr4:143273400-143299000	Weak transcription	Left Ventricle	heart
4	chr4:143274800-143285800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr4:143274800-143286200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:143274800-143288800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:143275200-143286000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:143275400-143285000	Weak transcription	A549	lung
9	chr4:143275400-143288000	Weak transcription	Aorta	Aorta
10	chr4:143275600-143286200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:143276200-143282600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr4:143276200-143285800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr4:143276200-143285800	Weak transcription	NHDF-Ad	bronchial
14	chr4:143276200-143289800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr4:143277000-143283800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:143277000-143285000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr4:143277000-143286200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:143277000-143288000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr4:143277000-143288000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr4:143277200-143286200	Weak transcription	Fetal Lung	lung
21	chr4:143277200-143288000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr4:143277800-143289800	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr4:143278200-143286200	Weak transcription	HMEC	breast
24	chr4:143278400-143283200	Weak transcription	Primary T cells from cord blood	blood
25	chr4:143278400-143284800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:143278400-143294200	Weak transcription	Stomach Mucosa	stomach
27	chr4:143278600-143284200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr4:143278800-143283200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:143278800-143284600	Weak transcription	Dnd41	blood
30	chr4:143279800-143282400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:143280200-143284000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr4:143280200-143284800	Weak transcription	HSMM	muscle
33	chr4:143280400-143283000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:143280400-143283400	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr4:143280400-143286000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr4:143280600-143284600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:143280600-143285000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr4:143280600-143287600	Weak transcription	Fetal Heart	heart
39	chr4:143281000-143283800	Weak transcription	NHEK	skin
40	chr4:143281200-143282800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr4:143281400-143283600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:143281600-143282400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr4:143281800-143282000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr4:143281800-143282200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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