Variant report

Variant	rs6441208
Chromosome Location	chr3:158299555-158299556
allele	A/T
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: 36 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12489730	0.83[CHD][hapmap];0.88[GIH][hapmap]
rs1560418	0.80[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];0.80[YRI][hapmap]
rs17630980	1.00[JPT][hapmap]
rs17643860	0.80[GIH][hapmap]
rs17697458	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs17699103	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs17699324	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap]
rs17699478	0.87[CHD][hapmap];0.92[GIH][hapmap]
rs17700122	0.87[CHD][hapmap];0.92[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];0.80[YRI][hapmap]
rs2307064	0.87[CHD][hapmap];0.92[GIH][hapmap]
rs3863076	0.80[GIH][hapmap]
rs3867391	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap]
rs6776901	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs6777231	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs6804230	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]
rs7610009	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6441208	LXN	cis	parietal	SCAN
rs6441208	GFM1	cis	Nerve Tibial	GTEx
rs6441208	GFM1	cis	parietal	SCAN
rs6441208	LXN	cis	cerebellum	SCAN
rs6441208	GFM1	cis	Muscle Skeletal	GTEx
rs6441208	LXN	cis	multi-tissue	Pritchard
rs6441208	GFM1	cis	cerebellum	SCAN
rs6441208	GFM1	cis	Thyroid	GTEx
rs6441208	GFM1	cis	Esophagus Mucosa	GTEx
rs6441208	KPNA4	cis	cerebellum	SCAN
rs6441208	GFM1	cis	Artery Tibial	GTEx
rs6441208	LXN	cis	lymphoblastoid	seeQTL

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	chr3:158299200-158299800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:158299400-158329400	Weak transcription	Left Ventricle	heart

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