Variant report

Variant	rs6425316
Chromosome Location	chr1:175045902-175045903
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:175037717..175040130-chr1:175044107..175046974,3	K562	blood:
2	chr1:175045192..175046870-chr15:101253779..101256143,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1108523	0.84[JPT][hapmap]
rs11578419	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11802280	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12691475	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12729551	0.83[JPT][hapmap]
rs12730537	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13373936	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1573758	0.83[JPT][hapmap]
rs1573759	0.84[JPT][hapmap]
rs17302506	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17374654	0.83[JPT][hapmap]
rs2072031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2072032	0.84[JPT][hapmap]
rs2105948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2213853	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2213854	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2861104	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs2861106	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs34142971	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34731331	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4408114	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4620493	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4651301	0.83[JPT][hapmap]
rs56105959	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57969863	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs58721108	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6656377	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6656523	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6683073	0.83[JPT][hapmap]
rs6683495	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703740	0.83[JPT][hapmap]
rs7515578	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9286900	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs929126	0.83[JPT][hapmap]

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	nsv1012861	chr1:175021780-175063160	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv535210	chr1:175021780-175063160	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv825487	chr1:175031609-175113572	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6425316	RABGAP1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175039800-175046600	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr1:175042400-175050600	Weak transcription	Spleen	Spleen
3	chr1:175043200-175057400	Weak transcription	Fetal Muscle Leg	muscle
4	chr1:175043200-175058600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr1:175043400-175046200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:175043800-175046000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:175044200-175046400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr1:175044200-175049400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:175044800-175047000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:175045400-175046200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:175045400-175049200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:175045600-175058400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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