Variant report

Variant	rs6683495
Chromosome Location	chr1:175042826-175042827
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	chr1:175041206..175043201-chr1:175056003..175057829,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11578419	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11802280	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12691475	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12730537	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13373936	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17302506	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2072031	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2105948	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2213853	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2213854	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34142971	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34731331	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4408114	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4620493	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56105959	0.88[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]
rs6425316	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656377	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6656523	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7515578	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9286900	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][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	nsv1011472	chr1:175013165-175042885	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
rs6683495	RABGAP1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 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	chr1:175040400-175043200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr1:175040600-175044000	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr1:175040800-175043000	Enhancers	Fetal Stomach	stomach
5	chr1:175041000-175043000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr1:175041000-175043000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:175041000-175043400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:175041000-175044000	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr1:175041000-175044200	Enhancers	H1 Cell Line	embryonic stem cell
10	chr1:175041000-175044200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:175041200-175043200	Enhancers	H9 Cell Line	embryonic stem cell
12	chr1:175041400-175043000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:175041400-175043000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr1:175041600-175043200	Enhancers	Fetal Brain Male	brain
15	chr1:175041800-175043200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:175041800-175044800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:175041800-175045000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr1:175042000-175043000	Enhancers	Fetal Brain Female	brain
19	chr1:175042000-175043400	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr1:175042400-175043000	Enhancers	Adipose Nuclei	Adipose
21	chr1:175042400-175043000	Enhancers	Stomach Smooth Muscle	stomach
22	chr1:175042400-175043200	Enhancers	Fetal Muscle Trunk	muscle
23	chr1:175042400-175043200	Enhancers	Fetal Muscle Leg	muscle
24	chr1:175042400-175043200	Enhancers	Dnd41	blood
25	chr1:175042400-175043800	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr1:175042400-175043800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:175042400-175044000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:175042400-175044200	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr1:175042400-175050600	Weak transcription	Spleen	Spleen
30	chr1:175042600-175043000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:175042600-175043000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
32	chr1:175042800-175043000	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr1:175042800-175043000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:175042800-175043000	Bivalent Enhancer	GM12878-XiMat	blood

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