Variant report

Variant	rs12562357
Chromosome Location	chr1:180534407-180534408
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:180530082..180533605-chr1:180534162..180536876,3	K562	blood:
2	chr1:180530731..180535452-chr1:180539258..180542430,4	K562	blood:
3	chr1:180533968..180536726-chr1:180538113..180540061,3	MCF-7	breast:
4	chr1:180529943..180534795-chr1:180578153..180581956,5	K562	blood:
5	chr1:180528019..180529576-chr1:180533585..180535526,2	K562	blood:
6	chr1:180524735..180527713-chr1:180532458..180534651,2	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-XPR1-2	chr1:180534387-180535654	XLOC_000477
2	lnc-XPR1-2	chr1:180534387-180535508	XLOC_000477
3	lnc-XPR1-2	chr1:180534387-180535654	ENSG00000236719
4	lnc-XPR1-2	chr1:180534387-180535634	XLOC_000477

No data

Variant related genes	Relation type
ENSG00000236719	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10798779	0.94[ASN][1000 genomes]
rs10798782	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs10914041	0.94[ASN][1000 genomes]
rs12028578	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12032249	0.94[ASN][1000 genomes]
rs12073348	0.85[EUR][1000 genomes]
rs12754682	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17373022	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4097353	0.89[ASN][1000 genomes]
rs6663339	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs67466592	0.89[EUR][1000 genomes]
rs72720958	0.91[EUR][1000 genomes]
rs7512134	0.83[CHD][hapmap]
rs9803871	0.91[ASN][1000 genomes]
rs9804047	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	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv947137	chr1:180531647-180537166	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180516600-180536800	Weak transcription	Psoas Muscle	Psoas
2	chr1:180530000-180535000	Enhancers	Left Ventricle	heart
3	chr1:180530800-180535200	Weak transcription	Pancreas	Pancrea
4	chr1:180531400-180537400	Enhancers	Fetal Brain Male	brain
5	chr1:180531600-180535000	Enhancers	Fetal Heart	heart
6	chr1:180532400-180534800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr1:180532600-180534600	Weak transcription	HUVEC	blood vessel
8	chr1:180532600-180536600	Enhancers	Fetal Brain Female	brain
9	chr1:180532600-180537000	Weak transcription	Aorta	Aorta
10	chr1:180532600-180539800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:180532600-180540400	Weak transcription	A549	lung
12	chr1:180532800-180534600	Weak transcription	HepG2	liver
13	chr1:180532800-180535000	Weak transcription	HSMMtube	muscle
14	chr1:180532800-180536400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:180532800-180539400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:180532800-180539600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:180532800-180539600	Weak transcription	HMEC	breast
18	chr1:180533000-180536000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:180533000-180536800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:180533000-180538600	Weak transcription	Osteobl	bone
21	chr1:180534000-180539400	Weak transcription	K562	blood
22	chr1:180534400-180534600	Flanking Active TSS	Right Atrium	heart
23	chr1:180534400-180534600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr1:180534400-180535000	Active TSS	Brain Substantia Nigra	brain
25	chr1:180534400-180535000	Enhancers	Right Ventricle	heart
26	chr1:180534400-180535400	Active TSS	Adipose Nuclei	Adipose
27	chr1:180534400-180536200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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