Variant report

Variant	rs1435642
Chromosome Location	chr3:158300221-158300222
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158298751..158301229-chr3:158359663..158362148,3	K562	blood:

Variant related genes	Relation type
ENSG00000168827	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1038886	0.86[ASN][1000 genomes]
rs1047366	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.84[MKK][hapmap];0.85[YRI][hapmap];0.87[ASN][1000 genomes]
rs1075551	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10936158	0.87[ASN][1000 genomes]
rs12107643	1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12496174	0.87[ASN][1000 genomes]
rs12639052	0.85[YRI][hapmap]
rs13074694	1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13324770	0.84[ASN][1000 genomes]
rs13325932	0.87[ASN][1000 genomes]
rs1369563	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1435643	0.85[CHB][hapmap]
rs1595028	0.95[CHB][hapmap]
rs1602760	0.86[ASN][1000 genomes]
rs1620229	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1656366	0.95[CHB][hapmap]
rs1656374	0.89[AFR][1000 genomes]
rs1656376	0.92[ASW][hapmap];0.95[CHB][hapmap];0.89[GIH][hapmap];0.83[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1656377	1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.86[YRI][hapmap];0.89[ASN][1000 genomes]
rs1714507	0.84[ASW][hapmap];0.95[CHB][hapmap];0.86[GIH][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.90[YRI][hapmap]
rs1714516	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1714518	0.95[CHB][hapmap]
rs1714524	0.90[AFR][1000 genomes]
rs17629360	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs17629390	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs17629414	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs17630086	0.85[CHB][hapmap]
rs1836688	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1864503	0.87[ASN][1000 genomes]
rs1864507	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[ASN][1000 genomes]
rs2115943	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2248924	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2276773	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2303909	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.84[MKK][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs2364274	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2566344	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2573179	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2731112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2731118	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2731120	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2731122	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28481597	0.88[ASN][1000 genomes]
rs2933550	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3765025	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3845272	0.90[ASN][1000 genomes]
rs3851361	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3851362	0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs3851363	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4680445	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4680449	0.91[ASN][1000 genomes]
rs4680451	0.87[ASN][1000 genomes]
rs4680452	0.87[ASN][1000 genomes]
rs4680453	0.90[ASN][1000 genomes]
rs4680457	0.86[ASN][1000 genomes]
rs4875	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs62287933	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6441206	0.95[CHB][hapmap]
rs6441212	0.91[ASN][1000 genomes]
rs6441220	0.86[ASN][1000 genomes]
rs6763812	0.86[ASN][1000 genomes]
rs6771248	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6772483	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.84[MKK][hapmap];0.86[YRI][hapmap];0.86[ASN][1000 genomes]
rs6777711	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6781342	0.88[ASN][1000 genomes]
rs6795376	0.95[CHB][hapmap]
rs6800914	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6802317	0.87[ASN][1000 genomes]
rs6803047	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6803608	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6804249	0.92[ASW][hapmap]
rs6804259	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7612250	0.85[CHB][hapmap]
rs7613814	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7613824	0.85[CHB][hapmap]
rs7620927	0.95[CHB][hapmap]
rs7621897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[ASN][1000 genomes]
rs7628293	0.85[CHB][hapmap]
rs7631310	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7648618	0.90[CHB][hapmap]
rs7653826	0.91[ASN][1000 genomes]
rs8455	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[ASN][1000 genomes]
rs891464	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.84[MKK][hapmap];0.86[YRI][hapmap];0.90[ASN][1000 genomes]
rs9810887	0.90[CHB][hapmap]
rs9819134	0.90[CHB][hapmap]
rs9819567	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs9819631	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9824985	0.87[ASN][1000 genomes]
rs9844502	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9848908	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9858318	0.90[CHB][hapmap]
rs9859129	0.90[CHB][hapmap]
rs9864508	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9883657	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1435642	LXN	cis	cerebellum	SCAN
rs1435642	GFM1	cis	cerebellum	SCAN
rs1435642	LXN	cis	parietal	SCAN
rs1435642	LXN	cis	lymphoblastoid	seeQTL
rs1435642	RP11-538P18.2	cis	Artery Tibial	GTEx
rs1435642	LXN	cis	multi-tissue	Pritchard
rs1435642	MLF1	cis	Esophagus Mucosa	GTEx
rs1435642	RSRC1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158290400-158324400	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:158292000-158315400	Weak transcription	Right Ventricle	heart
3	chr3:158297800-158312000	Weak transcription	Fetal Heart	heart
4	chr3:158299000-158301000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:158299400-158329400	Weak transcription	Left Ventricle	heart
6	chr3:158299800-158320400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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