Variant report

Variant	rs9387654
Chromosome Location	chr6:119802083-119802084
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:119800351..119802770-chr6:119806330..119807871,2	K562	blood:
2	chr6:119801119..119803739-chr6:119829063..119831730,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ASF1A-7	chr6:119801006-119804785	NONHSAT114718

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11153826	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12528127	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12529667	0.89[MEX][hapmap]
rs12530171	0.89[MEX][hapmap]
rs1342313	0.81[AMR][1000 genomes]
rs1909506	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs195057	0.84[MEX][hapmap]
rs195077	0.89[MEX][hapmap]
rs1995224	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2066351	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2153825	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2357505	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4945638	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4946416	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4946421	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4946428	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4946430	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58391013	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6900388	0.81[AMR][1000 genomes]
rs6925366	0.84[AMR][1000 genomes]
rs6935847	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6936821	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72952941	0.81[AMR][1000 genomes]
rs7761301	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7774019	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs885028	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9374789	0.89[MEX][hapmap]
rs9374797	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9374798	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9374799	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9374800	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9374801	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9374802	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9374803	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9385074	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9385075	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9387650	0.81[AMR][1000 genomes]
rs9398506	0.89[MEX][hapmap]
rs9401149	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1027904	chr6:119709488-120001986	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv533518	chr6:119712186-119998618	ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3442553	chr6:119742069-120076777	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv5455	chr6:119794976-119839636	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9387654	RAB4A	trans	lymphoblastoid	seeQTL
rs9387654	TGFBR3	trans	lymphoblastoid	seeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119797600-119805400	Weak transcription	Spleen	Spleen
2	chr6:119800000-119803000	Enhancers	K562	blood
3	chr6:119800200-119802200	Enhancers	Pancreatic Islets	Pancreatic Islet
4	chr6:119800400-119802600	Enhancers	Dnd41	blood
5	chr6:119800600-119802200	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr6:119801000-119802800	Enhancers	Primary hematopoietic stem cells	blood
7	chr6:119801000-119802800	Enhancers	Colon Smooth Muscle	Colon
8	chr6:119801000-119803800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:119801000-119803800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:119801000-119803800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:119801000-119804000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:119801000-119806800	Enhancers	Fetal Heart	heart
13	chr6:119801200-119802800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:119801200-119802800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:119801400-119802800	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr6:119801800-119802800	Weak transcription	Osteobl	bone
17	chr6:119801800-119805200	Weak transcription	Stomach Mucosa	stomach
18	chr6:119801800-119805400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr6:119802000-119805400	Weak transcription	Muscle Satellite Cultured Cells	--

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