Variant report

Variant	rs1249807
Chromosome Location	chr1:75839320-75839321
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	chr1:75826578..75828663-chr1:75838109..75841105,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10518500	0.94[CEU][hapmap]
rs11163461	0.89[CHD][hapmap];0.82[JPT][hapmap]
rs11163490	0.81[JPT][hapmap]
rs11163493	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs11163496	0.82[JPT][hapmap]
rs11804097	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs11806471	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11809429	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11811008	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12402118	0.82[CHD][hapmap]
rs1249777	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1249783	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1249794	0.82[ASW][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap]
rs1249796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1249797	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1249823	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1443846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17096508	0.80[CEU][hapmap]
rs17096860	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17096877	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs17584530	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1778454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1778459	0.82[CHB][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs2083868	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs2347215	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2347217	1.00[CHB][hapmap]
rs2972005	0.85[CHB][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs3845363	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs588830	0.81[CEU][hapmap]
rs590301	0.83[CEU][hapmap]
rs596515	0.82[CEU][hapmap]
rs598649	0.89[CEU][hapmap]
rs604745	0.82[CEU][hapmap]
rs617196	0.81[CEU][hapmap]
rs625357	0.83[CEU][hapmap]
rs629615	0.81[CEU][hapmap]
rs635184	0.81[CEU][hapmap]
rs639028	0.82[CEU][hapmap]
rs642923	0.83[CEU][hapmap]
rs648869	0.81[CEU][hapmap]
rs663620	0.81[CEU][hapmap]
rs664268	0.81[CEU][hapmap]
rs665545	0.87[CEU][hapmap]
rs6657734	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs6676696	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap]
rs671919	0.87[CEU][hapmap]
rs675962	0.82[CEU][hapmap]
rs681689	0.81[CEU][hapmap]
rs694025	0.81[CEU][hapmap]

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	esv3368999	chr1:75524762-75933220	Bivalent/Poised TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1013952	chr1:75716654-75936048	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv535004	chr1:75716654-75936048	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1455	chr1:75812377-75864182	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv508304	chr1:75838772-75857426	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1249807	SLC44A5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75831200-75841000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:75831400-75841400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:75833400-75841000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr1:75833600-75841200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:75836800-75841200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:75837400-75840200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:75837800-75841600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:75838200-75840600	Weak transcription	NHEK	skin
9	chr1:75838200-75841800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:75838400-75839800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:75838400-75840400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:75839000-75839800	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr1:75839000-75840400	Enhancers	Placenta	Placenta
14	chr1:75839200-75839800	Enhancers	K562	blood
15	chr1:75839200-75840200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:75839200-75840400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:75839200-75840400	Flanking Active TSS	HepG2	liver

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