Variant report

Variant	rs1489578
Chromosome Location	chr4:143331053-143331054
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:143329246..143331724-chr4:143394946..143397603,2	MCF-7	breast:
2	chr4:143327221..143331819-chr4:143394116..143397905,6	MCF-7	breast:
3	chr4:143325204..143328052-chr4:143329369..143331375,2	K562	blood:

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1158692	0.92[CEU][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap];0.91[TSI][hapmap]
rs11722756	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12511267	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13128245	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13135641	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13138212	0.92[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13140802	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13144939	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]
rs1391098	0.83[CEU][hapmap];0.80[JPT][hapmap]
rs1489577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1497389	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	0.92[CEU][hapmap];0.91[GIH][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap]
rs1497398	0.87[CEU][hapmap]
rs1565306	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17715707	1.00[ASW][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap]
rs1812174	0.83[CEU][hapmap];0.80[JPT][hapmap]
rs1982966	1.00[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2173209	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2306913	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2627802	1.00[LWK][hapmap]
rs2627804	1.00[LWK][hapmap]
rs2627806	0.85[AFR][1000 genomes]
rs2635424	0.92[CEU][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap];0.88[TSI][hapmap]
rs2635429	1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap]
rs2646085	0.83[CEU][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs2646091	1.00[YRI][hapmap]
rs34830426	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35151914	0.87[ASN][1000 genomes]
rs3775703	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3775705	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775706	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775710	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775711	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775716	1.00[YRI][hapmap]
rs3775718	1.00[ASW][hapmap]
rs3775720	1.00[ASW][hapmap]
rs3822157	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6820232	1.00[YRI][hapmap]
rs6825345	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs716762	0.92[CEU][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap];0.88[TSI][hapmap]
rs724131	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs72724560	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7699598	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs881611	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931419	0.83[CEU][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs983767	0.96[AMR][1000 genomes];0.86[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	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
3	nsv968011	chr4:143325315-143333139	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1489578	LSM6	cis	cerebellum	SCAN
rs1489578	C4orf49	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143327600-143331200	Enhancers	NHEK	skin
2	chr4:143327600-143335600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:143327800-143335600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:143328400-143331600	Enhancers	Primary T cells fromperipheralblood	blood
5	chr4:143328400-143331600	Enhancers	HMEC	breast
6	chr4:143328600-143335200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:143328600-143336400	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr4:143328800-143332600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr4:143328800-143334200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:143329000-143334000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr4:143329000-143334000	Weak transcription	HSMMtube	muscle
12	chr4:143329000-143334600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:143329000-143335000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:143329000-143335800	Weak transcription	Fetal Muscle Leg	muscle
15	chr4:143329000-143336000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr4:143329000-143336200	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr4:143329000-143336600	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr4:143329000-143338200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr4:143329000-143350000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr4:143329600-143331400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:143329800-143337200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr4:143330000-143334000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:143330000-143334600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:143330000-143334800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:143330000-143335000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:143330000-143335600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr4:143330000-143337400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:143330000-143338000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr4:143330200-143344800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:143330400-143333800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr4:143330400-143334000	Weak transcription	A549	lung
32	chr4:143330400-143334000	Weak transcription	HSMM	muscle
33	chr4:143330400-143334600	Weak transcription	Primary T cells from cord blood	blood
34	chr4:143330400-143337400	Weak transcription	NHDF-Ad	bronchial
35	chr4:143330600-143331200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr4:143330600-143332200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:143330600-143334600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr4:143330600-143334600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:143330800-143331800	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr4:143331000-143331200	Enhancers	Thymus	Thymus
41	chr4:143331000-143332800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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