Variant report

Variant	rs5745323
Chromosome Location	chr1:76269372-76269373
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	chr1:76261350..76264622-chr1:76266576..76269506,4	MCF-7	breast:
2	chr1:76259028..76263655-chr1:76264104..76269438,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137955	Chromatin interaction
ENSG00000057468	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1001160	1.00[JPT][hapmap]
rs10873729	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10873733	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10873797	1.00[JPT][hapmap]
rs11161598	0.84[EUR][1000 genomes]
rs11161688	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161718	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11161848	1.00[JPT][hapmap]
rs11161902	1.00[JPT][hapmap]
rs11163967	1.00[JPT][hapmap]
rs1144340	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146598	0.81[EUR][1000 genomes]
rs1146617	0.83[EUR][1000 genomes]
rs1146631	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1146632	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1146634	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146636	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146637	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1146643	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146644	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578480	1.00[JPT][hapmap]
rs11588643	1.00[JPT][hapmap]
rs1159215	1.00[JPT][hapmap]
rs12043473	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs12092388	0.84[EUR][1000 genomes]
rs12130832	1.00[JPT][hapmap]
rs12131344	1.00[JPT][hapmap]
rs12132750	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12142247	1.00[JPT][hapmap]
rs12734931	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463812	1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1498311	1.00[JPT][hapmap]
rs1628063	1.00[JPT][hapmap]
rs1630587	1.00[JPT][hapmap]
rs1689270	1.00[JPT][hapmap]
rs17647178	1.00[JPT][hapmap]
rs1770889	1.00[JPT][hapmap]
rs1796813	1.00[JPT][hapmap]
rs1796815	1.00[JPT][hapmap]
rs1796827	1.00[JPT][hapmap]
rs1856791	1.00[JPT][hapmap]
rs2029682	1.00[JPT][hapmap]
rs4638068	1.00[JPT][hapmap]
rs5745325	1.00[JPT][hapmap]
rs5745331	1.00[JPT][hapmap]
rs5745347	1.00[JPT][hapmap]
rs5745383	1.00[JPT][hapmap]
rs5745394	1.00[JPT][hapmap]
rs5745430	1.00[JPT][hapmap]
rs5745543	1.00[JPT][hapmap]
rs5745545	1.00[JPT][hapmap]
rs5745547	1.00[JPT][hapmap]
rs6593520	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs6593521	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs6656501	1.00[JPT][hapmap]
rs721204	1.00[JPT][hapmap]
rs7552289	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1795237	chr1:76268573-76383565	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5745323	RABGGTB	Cis_1M	lymphoblastoid	RTeQTL
rs5745323	MSH4	cis	Esophagus Muscularis	GTEx
rs5745323	MSH4	cis	Muscle Skeletal	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76262400-76269400	Weak transcription	NHDF-Ad	bronchial
2	chr1:76262400-76273200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:76262400-76282800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:76262600-76288800	Weak transcription	Brain Substantia Nigra	brain
5	chr1:76262600-76294600	Weak transcription	Primary B cells from cord blood	blood
6	chr1:76263000-76269400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:76263000-76276600	Weak transcription	Gastric	stomach
8	chr1:76263000-76287400	Weak transcription	Aorta	Aorta
9	chr1:76263000-76289000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:76263000-76296200	Weak transcription	Ovary	ovary
11	chr1:76263200-76277000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:76263400-76289000	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:76263600-76284000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr1:76264000-76269400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:76264000-76270600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:76264000-76274200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:76264000-76277000	Weak transcription	HUVEC	blood vessel
18	chr1:76264200-76274800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:76264200-76279800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:76264200-76291400	Weak transcription	Psoas Muscle	Psoas
21	chr1:76264600-76273600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr1:76264600-76278000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:76264600-76288600	Weak transcription	Left Ventricle	heart
24	chr1:76264800-76277000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:76264800-76288600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:76264800-76288600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:76265600-76270200	Weak transcription	Adipose Nuclei	Adipose
28	chr1:76266000-76272800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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