Variant report

Variant	rs6804230
Chromosome Location	chr3:158314188-158314189
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158311702..158314376-chr3:158337102..158338612,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12489730	0.83[CHD][hapmap];0.92[GIH][hapmap]
rs1560417	0.83[GIH][hapmap]
rs1560418	0.84[GIH][hapmap]
rs1595027	1.00[CHB][hapmap]
rs16829044	1.00[CHB][hapmap]
rs16829064	1.00[CHB][hapmap]
rs16829102	1.00[CHB][hapmap]
rs16829105	1.00[CHB][hapmap]
rs1714522	1.00[CHB][hapmap]
rs17630607	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17630980	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17643860	0.84[GIH][hapmap]
rs17697458	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17698494	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17699103	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17699324	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17699478	0.87[CHD][hapmap];0.96[GIH][hapmap]
rs17700122	0.87[CHD][hapmap];0.96[GIH][hapmap]
rs1978780	0.88[CHB][hapmap]
rs2196357	0.88[CHB][hapmap]
rs2304408	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2307064	0.87[CHD][hapmap];0.96[GIH][hapmap]
rs28372852	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35057010	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3863076	0.84[GIH][hapmap]
rs3867391	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs55666734	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56075263	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56089835	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56148431	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56167308	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56242377	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60942689	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62286650	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62286654	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62287938	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62288301	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62288303	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62288305	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62288306	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62288307	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62288344	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62288345	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6441208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap]
rs6776901	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6777231	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7610009	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7628497	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7633713	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
8	nsv869644	chr3:158308783-158426343	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6804230	KPNA4	cis	cerebellum	SCAN
rs6804230	GFM1	cis	Thyroid	GTEx
rs6804230	GFM1	cis	cerebellum	SCAN
rs6804230	LXN	Cis_1M	lymphoblastoid	RTeQTL
rs6804230	LXN	cis	multi-tissue	Pritchard
rs6804230	GFM1	cis	Muscle Skeletal	GTEx
rs6804230	LXN	cis	parietal	SCAN
rs6804230	GFM1	cis	parietal	SCAN
rs6804230	GFM1	cis	Artery Tibial	GTEx
rs6804230	LXN	cis	cerebellum	SCAN
rs6804230	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs6804230	LXN	cis	lymphoblastoid	seeQTL

Chromatin state (count:17 , 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	chr3:158299400-158329400	Weak transcription	Left Ventricle	heart
4	chr3:158299800-158320400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:158302600-158315200	Weak transcription	Fetal Lung	lung
6	chr3:158302600-158316400	Weak transcription	Psoas Muscle	Psoas
7	chr3:158303600-158320200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:158304200-158320200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:158304600-158323400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:158305000-158322600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:158305600-158330200	Weak transcription	Brain Anterior Caudate	brain
12	chr3:158305800-158328800	Weak transcription	Ovary	ovary
13	chr3:158307600-158322800	Weak transcription	Aorta	Aorta
14	chr3:158309200-158322000	Weak transcription	Fetal Brain Male	brain
15	chr3:158311400-158329800	Weak transcription	Brain Angular Gyrus	brain
16	chr3:158313200-158322000	Weak transcription	Fetal Heart	heart
17	chr3:158313600-158318200	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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