Variant report

Variant	rs12959303
Chromosome Location	chr18:9648419-9648420
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9643273..9646084-chr18:9646208..9649235,5	K562	blood:
2	chr18:9638107..9640165-chr18:9648278..9650768,2	K562	blood:
3	chr18:9646205..9649195-chr18:9657550..9659547,2	K562	blood:
4	chr18:9647445..9649188-chr18:9652519..9654755,2	K562	blood:
5	chr18:9645776..9648945-chr18:9653255..9655530,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RAB31-1	chr18:9647984-9648542	XLOC_012623

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12957571	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12960645	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12970514	0.84[CEU][hapmap]
rs16955402	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs2061136	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061137	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2061139	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4384658	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55818445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609427	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs62080347	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs663000	0.84[CEU][hapmap];0.82[JPT][hapmap]

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	esv3693417	chr18:9512985-9693638	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv458024	chr18:9558240-9828448	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv576448	chr18:9558240-9828448	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv576449	chr18:9623052-9700382	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12959303	SEH1L	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9639200-9663400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:9643400-9649400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr18:9643800-9649800	Weak transcription	Fetal Muscle Leg	muscle
4	chr18:9644400-9648800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr18:9644400-9649200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr18:9644400-9649800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr18:9644800-9649400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr18:9645200-9649000	Weak transcription	NHDF-Ad	bronchial
9	chr18:9646400-9649000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr18:9646800-9649000	Enhancers	HepG2	liver
11	chr18:9646800-9649200	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr18:9647200-9648800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr18:9647400-9649600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr18:9647400-9649600	Enhancers	HMEC	breast
15	chr18:9647600-9648600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr18:9647600-9648800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr18:9647600-9649000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr18:9647600-9649000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr18:9647600-9649600	Enhancers	NH-A	brain
20	chr18:9647600-9650000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr18:9647800-9648800	Enhancers	Primary hematopoietic stem cells	blood
22	chr18:9647800-9649200	Flanking Active TSS	NHEK	skin
23	chr18:9647800-9649600	Weak transcription	Esophagus	oesophagus
24	chr18:9648000-9650000	Enhancers	GM12878-XiMat	blood
25	chr18:9648200-9648600	Enhancers	H9 Cell Line	embryonic stem cell
26	chr18:9648200-9649000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr18:9648200-9651600	Weak transcription	Placenta	Placenta
28	chr18:9648200-9653000	Weak transcription	Hela-S3	cervix
29	chr18:9648200-9653200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr18:9648200-9653200	Weak transcription	HUVEC	blood vessel
31	chr18:9648200-9653400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr18:9648400-9648800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr18:9648400-9648800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr18:9648400-9649200	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr18:9648400-9649600	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr18:9648400-9649800	Enhancers	A549	lung

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