Variant report

Variant	rs1875513
Chromosome Location	chr5:14657062-14657063
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	RELA	chr5:14657020-14657866	GM12878	blood:	n/a	chr5:14657233-14657242 chr5:14657233-14657242
2	ATF2	chr5:14656821-14657313	GM12878	blood:	n/a	n/a
3	NFIC	chr5:14656864-14658073	GM12878	blood:	n/a	n/a
4	FOXM1	chr5:14657020-14657449	GM12878	blood:	n/a	n/a
5	RUNX3	chr5:14657014-14657875	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:14654188..14656036-chr5:14656686..14658192,2	MCF-7	breast:
2	chr5:14654818..14657661-chr5:14662686..14665477,2	MCF-7	breast:
3	chr5:14652517..14654606-chr5:14656081..14657786,2	K562	blood:

Variant related genes	Relation type
EEF1A1P13	TF binding region
ENSG00000250182	Chromatin interaction
ENSG00000261360	Chromatin interaction
ENSG00000154124	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs13189930	0.87[JPT][hapmap]
rs149493	0.92[ASN][1000 genomes]
rs149617	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs152788	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs153829	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs153830	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs166127	0.81[ASN][1000 genomes]
rs183681	0.80[ASN][1000 genomes]
rs2455402	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs250435	0.81[ASN][1000 genomes]
rs250439	0.92[ASN][1000 genomes]
rs250440	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs258290	0.84[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.89[ASN][1000 genomes]
rs258374	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs25945	1.00[JPT][hapmap]
rs25951	1.00[JPT][hapmap]
rs25952	1.00[JPT][hapmap]
rs25983	0.87[JPT][hapmap]
rs25986	0.93[JPT][hapmap]
rs25987	0.93[JPT][hapmap]
rs25988	0.93[JPT][hapmap]
rs25992	0.93[JPT][hapmap]
rs26307	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs27356	0.87[JPT][hapmap];0.89[YRI][hapmap]
rs27911	0.93[JPT][hapmap]
rs28004	1.00[JPT][hapmap]
rs31920	1.00[JPT][hapmap]
rs31922	0.84[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.93[ASN][1000 genomes]
rs31923	1.00[JPT][hapmap]
rs31925	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs31926	1.00[JPT][hapmap]
rs31928	1.00[JPT][hapmap]
rs31929	1.00[JPT][hapmap]
rs31930	0.93[JPT][hapmap]
rs31968	0.94[ASW][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3853119	0.94[ASN][1000 genomes]
rs3866215	1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs42358	1.00[JPT][hapmap]
rs42681	1.00[JPT][hapmap]
rs456180	0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs459467	0.83[ASN][1000 genomes]
rs466880	0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4702043	0.84[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6554855	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6554856	0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6872954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs745328	0.93[JPT][hapmap]
rs95492	0.93[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv830211	chr5:14474675-14675776	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1032951	chr5:14529579-14667342	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv528770	chr5:14655699-14657062	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3322102	chr5:14656995-14657294	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1875513	DNAH5	cis	parietal	SCAN
rs1875513	FAM105B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14655200-14663800	Weak transcription	Pancreas	Pancrea
2	chr5:14655600-14659800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:14655600-14659800	Weak transcription	NHEK	skin
4	chr5:14655600-14661200	Weak transcription	Primary T cells from cord blood	blood
5	chr5:14655600-14663400	Weak transcription	Fetal Thymus	thymus
6	chr5:14655800-14663000	Weak transcription	Dnd41	blood
7	chr5:14656600-14658400	Enhancers	GM12878-XiMat	blood
8	chr5:14657000-14657400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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