Variant report

Variant	rs17101052
Chromosome Location	chr1:78370991-78370992
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	chr1:78365620..78368344-chr1:78369014..78371823,2	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1135921	1.00[AMR][1000 genomes]
rs17100850	1.00[EUR][1000 genomes]
rs17100941	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs17101048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17101082	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.98[ASN][1000 genomes]
rs17101109	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2228247	0.87[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2296455	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.98[ASN][1000 genomes]
rs28362659	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28362660	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34128192	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3767026	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3767027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56325960	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59087988	1.00[ASN][1000 genomes]
rs72685391	0.91[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	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1006600	chr1:78222312-78384009	Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv535011	chr1:78222312-78384009	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17101052	NEXN	cis	lymphoblastoid	seeQTL
rs17101052	DDX6	trans	brain	seeQTL
rs17101052	FUBP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78355800-78383800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr1:78355800-78386200	Weak transcription	Fetal Intestine Small	intestine
3	chr1:78356200-78408600	Weak transcription	HMEC	breast
4	chr1:78356400-78396000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:78357400-78384400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:78357800-78371000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:78359200-78382400	Weak transcription	Left Ventricle	heart
8	chr1:78359800-78383800	Weak transcription	Fetal Lung	lung
9	chr1:78360600-78384200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:78361800-78372400	Weak transcription	Pancreas	Pancrea
11	chr1:78362400-78383200	Weak transcription	Fetal Muscle Leg	muscle
12	chr1:78362400-78383800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:78362400-78384000	Weak transcription	Fetal Stomach	stomach
14	chr1:78366600-78371600	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr1:78366800-78371200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr1:78366800-78372400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:78366800-78375600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:78366800-78381400	Weak transcription	Osteobl	bone
19	chr1:78366800-78382600	Weak transcription	NHLF	lung
20	chr1:78366800-78383600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:78366800-78383800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:78366800-78384000	Weak transcription	Aorta	Aorta
23	chr1:78367000-78375200	Weak transcription	Fetal Heart	heart
24	chr1:78367000-78378000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:78367000-78382400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:78367000-78407000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:78367400-78382200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:78367600-78372600	Weak transcription	Colon Smooth Muscle	Colon
29	chr1:78367600-78383800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:78367600-78383800	Weak transcription	Right Ventricle	heart
31	chr1:78369000-78371000	Weak transcription	HSMM	muscle
32	chr1:78369400-78372800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:78369600-78381400	Weak transcription	NH-A	brain
34	chr1:78370000-78371000	Weak transcription	Psoas Muscle	Psoas
35	chr1:78370200-78382400	Weak transcription	HSMMtube	muscle
36	chr1:78370600-78371600	Enhancers	Right Atrium	heart
37	chr1:78370600-78382400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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