Variant report

Variant	rs62287933
Chromosome Location	chr3:158290565-158290566
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr3:158288657-158290566	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr3:158289720-158290582	H1-hESC	embryonic stem cell:	n/a	n/a
3	E2F6	chr3:158288648-158290616	H1-hESC	embryonic stem cell:	n/a	chr3:158288898-158288907 chr3:158288900-158288909
4	MAX	chr3:158289774-158290579	H1-hESC	embryonic stem cell:	n/a	n/a
5	E2F6	chr3:158289647-158290580	K562	blood:	n/a	n/a
6	POLR2A	chr3:158290372-158290642	MCF-7	breast:	n/a	n/a
7	MYC	chr3:158290532-158290622	MCF-7	breast:	n/a	n/a
8	E2F6	chr3:158288630-158291153	K562	blood:	n/a	chr3:158288898-158288907 chr3:158288900-158288909
9	POLR2A	chr3:158288629-158290805	K562	blood:	n/a	n/a
10	ZNF263	chr3:158289935-158290802	HEK293-T-REx	kidney:	n/a	chr3:158290260-158290281 chr3:158290648-158290657 chr3:158290303-158290324

No.	Distal block	Cell Line	Cell type
1	chr3:158257580..158259389-chr3:158289106..158290845,2	K562	blood:
2	chr3:158284750..158291147-chr3:158359832..158364955,8	K562	blood:
3	chr3:158257580..158259170-chr3:158289106..158290622,2	K562	blood:
4	chr3:158289477..158292573-chr3:158361739..158363921,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RSRC1-1	chr3:158290246-158290605	l_2518_chr3:158290245-158301620_heart

Variant related genes	Relation type
ENSG00000243150	TF binding region
ENSG00000168827	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1038886	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1047366	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1075551	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10936158	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12107643	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12496174	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13074694	0.81[ASN][1000 genomes]
rs13324770	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13325932	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1369563	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1435642	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1602760	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1620229	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1656374	0.81[AFR][1000 genomes]
rs1656377	0.88[ASN][1000 genomes]
rs1714516	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1714524	0.82[AFR][1000 genomes]
rs17629360	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17629390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17629414	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1836688	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1864503	0.86[ASN][1000 genomes]
rs1864507	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2115943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2248924	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2276773	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2303909	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2364274	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2566344	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2573179	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2731112	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2731118	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2731120	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2731122	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs28481597	0.85[ASN][1000 genomes]
rs2933550	0.89[ASN][1000 genomes]
rs3765025	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3845272	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3851361	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3851363	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4680445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680449	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4680451	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4680452	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4680453	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4680457	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4875	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6441212	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6441220	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6763812	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6771248	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6772483	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6777711	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6781342	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6800914	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6802317	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6803047	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6803608	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6804259	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73154344	0.80[ASN][1000 genomes]
rs7613814	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7621897	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7631310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7653826	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8455	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs891464	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9819567	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9819631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9824985	0.84[ASN][1000 genomes]
rs9844502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9848908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9864508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1014381	chr3:158070451-158350118	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv877690	chr3:158184263-158296916	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv916167	chr3:158240540-158320581	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv877691	chr3:158245883-158359667	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1013242	chr3:158275578-158305894	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1013112	chr3:158280085-158301728	Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1001944	chr3:158280085-158305210	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv999408	chr3:158280085-158316431	Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv3327979	chr3:158288708-158291006	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62287933	LXN	Cis_1M	lymphoblastoid	RTeQTL
rs62287933	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs62287933	MLF1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158288200-158290600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:158288400-158292000	Active TSS	Right Atrium	heart
3	chr3:158288600-158290600	Active TSS	Left Ventricle	heart
4	chr3:158288800-158291000	Active TSS	Brain Anterior Caudate	brain
5	chr3:158288800-158291000	Active TSS	Fetal Heart	heart
6	chr3:158289400-158291000	Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr3:158289600-158290600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
8	chr3:158289600-158290600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:158289600-158290600	Weak transcription	Psoas Muscle	Psoas
10	chr3:158289600-158290800	Enhancers	Fetal Brain Male	brain
11	chr3:158289600-158290800	Enhancers	Fetal Muscle Trunk	muscle
12	chr3:158289600-158290800	Enhancers	Ovary	ovary
13	chr3:158289600-158291000	Enhancers	Esophagus	oesophagus
14	chr3:158289800-158290600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:158289800-158290800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:158289800-158291000	Weak transcription	HSMM	muscle
17	chr3:158290000-158290600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:158290000-158290800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:158290000-158290800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
20	chr3:158290000-158290800	Enhancers	Lung	lung
21	chr3:158290200-158290600	Enhancers	Fetal Stomach	stomach
22	chr3:158290200-158290600	Flanking Active TSS	Right Ventricle	heart
23	chr3:158290200-158290800	Enhancers	Brain Hippocampus Middle	brain
24	chr3:158290200-158291000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr3:158290400-158290600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:158290400-158290600	Enhancers	Gastric	stomach
27	chr3:158290400-158290600	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr3:158290400-158290800	Enhancers	Brain Germinal Matrix	brain
29	chr3:158290400-158291000	Enhancers	Stomach Smooth Muscle	stomach
30	chr3:158290400-158292000	Enhancers	K562	blood
31	chr3:158290400-158324400	Weak transcription	Colon Smooth Muscle	Colon

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