Variant report

Variant	rs2673772
Chromosome Location	chr5:127090699-127090700
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:126983791..126986140-chr5:127090604..127092155,2	MCF-7	breast:
2	chr5:127089564..127091502-chr5:127418692..127420552,2	MCF-7	breast:
3	chr5:127089663..127092388-chr5:127102893..127105245,2	K562	blood:

Variant related genes	Relation type
ENSG00000205279	Chromatin interaction
ENSG00000245937	Chromatin interaction
ENSG00000064651	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10041967	0.83[EUR][1000 genomes]
rs10061252	0.82[EUR][1000 genomes]
rs1007623	0.83[EUR][1000 genomes]
rs10519953	1.00[CEU][hapmap];0.90[TSI][hapmap]
rs10519960	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1086523	0.82[EUR][1000 genomes]
rs1086525	0.82[EUR][1000 genomes]
rs1086526	0.82[EUR][1000 genomes]
rs1086527	0.84[EUR][1000 genomes]
rs1086529	0.82[EUR][1000 genomes]
rs1086530	0.81[EUR][1000 genomes]
rs1086531	0.84[EUR][1000 genomes]
rs1086532	0.84[EUR][1000 genomes]
rs1086533	0.81[EUR][1000 genomes]
rs1086534	0.82[EUR][1000 genomes]
rs1088167	0.81[EUR][1000 genomes]
rs10900792	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1092720	0.81[EUR][1000 genomes]
rs11241938	0.83[EUR][1000 genomes]
rs11241939	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11241942	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11950864	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11957799	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1213827	0.83[EUR][1000 genomes]
rs1228156	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1234542	0.83[EUR][1000 genomes]
rs12652197	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12653785	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1399829	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1421747	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1432958	0.84[EUR][1000 genomes]
rs1515640	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1560673	0.95[CEU][hapmap];0.88[TSI][hapmap]
rs173580	0.83[EUR][1000 genomes]
rs173581	0.84[EUR][1000 genomes]
rs173582	0.82[EUR][1000 genomes]
rs1816404	0.83[EUR][1000 genomes]
rs1816405	0.83[EUR][1000 genomes]
rs1849938	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs187461	0.83[EUR][1000 genomes]
rs1897525	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193736	0.83[EUR][1000 genomes]
rs248689	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[TSI][hapmap]
rs248692	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[TSI][hapmap]
rs248709	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs248711	0.84[EUR][1000 genomes]
rs248712	0.82[EUR][1000 genomes]
rs248713	0.84[EUR][1000 genomes]
rs248715	0.82[EUR][1000 genomes]
rs248716	0.85[EUR][1000 genomes]
rs248717	0.84[EUR][1000 genomes]
rs248718	0.83[EUR][1000 genomes]
rs248720	0.81[EUR][1000 genomes]
rs248721	0.81[EUR][1000 genomes]
rs248722	0.85[EUR][1000 genomes]
rs248724	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs248730	0.83[EUR][1000 genomes]
rs248731	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs248732	0.83[EUR][1000 genomes]
rs248733	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs248735	0.83[EUR][1000 genomes]
rs248737	0.82[EUR][1000 genomes]
rs248738	0.83[EUR][1000 genomes]
rs248739	0.83[EUR][1000 genomes]
rs248740	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs248741	0.83[EUR][1000 genomes]
rs248742	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2569142	0.84[EUR][1000 genomes]
rs2569144	0.84[EUR][1000 genomes]
rs2569146	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2569148	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2673749	0.83[EUR][1000 genomes]
rs2673750	0.81[EUR][1000 genomes]
rs2673763	0.84[EUR][1000 genomes]
rs4361571	0.82[EUR][1000 genomes]
rs54201	0.83[EUR][1000 genomes]
rs57883466	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59513079	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62373501	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62373502	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6595789	0.85[EUR][1000 genomes]
rs7714847	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs790827	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs791071	0.82[EUR][1000 genomes]
rs791072	0.82[EUR][1000 genomes]
rs791073	0.81[EUR][1000 genomes]
rs791074	0.84[EUR][1000 genomes]
rs809349	0.82[EUR][1000 genomes]
rs812059	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs899190	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv830480	chr5:126964751-127124522	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2673772	SLC12A2	cis	cerebellum	SCAN
rs2673772	LYRM7	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127076000-127094800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:127088600-127090800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:127089000-127090800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:127089600-127090800	Enhancers	NH-A	brain
5	chr5:127089800-127090800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:127090000-127090800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:127090000-127090800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:127090000-127090800	Enhancers	Gastric	stomach
9	chr5:127090000-127090800	Enhancers	Ovary	ovary
10	chr5:127090000-127090800	Enhancers	Pancreas	Pancrea
11	chr5:127090000-127091000	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr5:127090000-127095000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:127090200-127090800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr5:127090200-127090800	Enhancers	Stomach Mucosa	stomach
15	chr5:127090200-127093400	Weak transcription	Fetal Intestine Large	intestine
16	chr5:127090200-127097000	Weak transcription	Fetal Lung	lung
17	chr5:127090400-127090800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:127090400-127090800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:127090400-127093400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr5:127090400-127093600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr5:127090600-127093400	Weak transcription	HSMMtube	muscle
22	chr5:127090600-127093600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr5:127090600-127093600	Weak transcription	Stomach Smooth Muscle	stomach

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