Variant report

Variant	rs41267628
Chromosome Location	chr1:180534878-180534879
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:5)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:180513656..180516816-chr1:180534714..180539709,4	K562	blood:
2	chr1:180530082..180533605-chr1:180534162..180536876,3	K562	blood:
3	chr1:180530731..180535452-chr1:180539258..180542430,4	K562	blood:
4	chr1:180533968..180536726-chr1:180538113..180540061,3	MCF-7	breast:
5	chr1:180528019..180529576-chr1:180533585..180535526,2	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
ENSG00000266683	Chromatin interaction
ENSG00000236719	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12565152	0.91[AMR][1000 genomes]
rs2153327	0.91[AMR][1000 genomes]
rs2331742	0.91[AMR][1000 genomes]
rs41267632	1.00[AFR][1000 genomes]
rs41267634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652510	0.91[AMR][1000 genomes]
rs61809269	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61809270	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61809271	1.00[AFR][1000 genomes]
rs61809273	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61809274	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61809275	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61809276	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61811627	0.91[AMR][1000 genomes]
rs61811628	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61811630	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61811631	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61811635	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6425647	0.91[AMR][1000 genomes]
rs6665615	0.91[AMR][1000 genomes]
rs946634	0.91[AMR][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	chr1:180532600-180536600	Enhancers	Fetal Brain Female	brain
7	chr1:180532600-180537000	Weak transcription	Aorta	Aorta
8	chr1:180532600-180539800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:180532600-180540400	Weak transcription	A549	lung
10	chr1:180532800-180535000	Weak transcription	HSMMtube	muscle
11	chr1:180532800-180536400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:180532800-180539400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:180532800-180539600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:180532800-180539600	Weak transcription	HMEC	breast
15	chr1:180533000-180536000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:180533000-180536800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:180533000-180538600	Weak transcription	Osteobl	bone
18	chr1:180534000-180539400	Weak transcription	K562	blood
19	chr1:180534400-180535000	Active TSS	Brain Substantia Nigra	brain
20	chr1:180534400-180535000	Enhancers	Right Ventricle	heart
21	chr1:180534400-180535400	Active TSS	Adipose Nuclei	Adipose
22	chr1:180534400-180536200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr1:180534600-180535200	Active TSS	Right Atrium	heart
24	chr1:180534600-180535200	Enhancers	HepG2	liver
25	chr1:180534600-180535400	Enhancers	Fetal Stomach	stomach
26	chr1:180534600-180537000	Enhancers	HUVEC	blood vessel
27	chr1:180534800-180535400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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