Variant report

Variant	rs4653639
Chromosome Location	chr1:225633824-225633825
allele	C/G
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:225633322..225636010-chr1:226185928..226188018,2	K562	blood:
2	chr1:225632657..225635050-chr1:226182326..226184522,2	MCF-7	breast:
3	chr1:225624234..225625837-chr1:225632480..225634509,2	K562	blood:
4	chr1:225632160..225634552-chr1:225642936..225645932,3	K562	blood:
5	chr1:225614179..225618111-chr1:225627420..225635153,13	K562	blood:
6	chr1:225609559..225620018-chr1:225630046..225635440,23	K562	blood:
7	chr1:225617914..225620224-chr1:225632867..225635155,3	MCF-7	breast:
8	chr1:225631906..225634098-chr1:225666664..225668819,2	K562	blood:
9	chr1:225633065..225638606-chr1:225639136..225643843,7	MCF-7	breast:
10	chr1:225629715..225632156-chr1:225633081..225634899,2	MCF-7	breast:
11	chr1:225625909..225628498-chr1:225632163..225635027,3	MCF-7	breast:
12	chr1:225632782..225636036-chr1:225646050..225649453,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143815	Chromatin interaction
ENSG00000143751	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10753406	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10799311	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10799314	0.83[AMR][1000 genomes]
rs10799317	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10799318	0.82[ASN][1000 genomes]
rs10915828	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915830	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10915833	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10915839	0.85[ASN][1000 genomes]
rs11584675	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3856156	0.80[AMR][1000 genomes]
rs4653637	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4653643	0.81[ASN][1000 genomes]
rs6426076	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6426077	0.84[ASN][1000 genomes]
rs6668770	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6697783	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6702452	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6702538	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6702555	0.85[ASN][1000 genomes]
rs6751	0.82[ASN][1000 genomes]
rs7515907	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7515939	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7524766	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7541598	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7549456	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7555553	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs947034	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv34905	chr1:225631404-225676582	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4653639	LBR	cis	Artery Tibial	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225625400-225636000	Enhancers	Colon Smooth Muscle	Colon
2	chr1:225626000-225636200	Enhancers	Fetal Intestine Large	intestine
3	chr1:225629200-225636400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr1:225629400-225635600	Enhancers	Primary hematopoietic stem cells	blood
5	chr1:225629400-225635600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:225629600-225634000	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr1:225629600-225634200	Enhancers	Spleen	Spleen
8	chr1:225629800-225634800	Enhancers	HUVEC	blood vessel
9	chr1:225630200-225634600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:225630200-225635200	Enhancers	Liver	Liver
11	chr1:225630200-225636400	Enhancers	Fetal Intestine Small	intestine
12	chr1:225630800-225636600	Enhancers	Fetal Muscle Leg	muscle
13	chr1:225631000-225634400	Enhancers	Fetal Muscle Trunk	muscle
14	chr1:225631200-225635000	Weak transcription	Psoas Muscle	Psoas
15	chr1:225631400-225634200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:225632200-225634000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:225632200-225634000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr1:225632200-225635800	Enhancers	Fetal Stomach	stomach
19	chr1:225632200-225637800	Enhancers	Stomach Mucosa	stomach
20	chr1:225632400-225634000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:225632400-225634000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:225632400-225634000	Enhancers	NHLF	lung
23	chr1:225632400-225634600	Enhancers	NHEK	skin
24	chr1:225632400-225635800	Enhancers	Placenta	Placenta
25	chr1:225632400-225636200	Enhancers	Fetal Lung	lung
26	chr1:225632600-225634000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:225632600-225634000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr1:225632600-225634200	Enhancers	HMEC	breast
29	chr1:225632600-225634400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:225632600-225634400	Enhancers	Pancreas	Pancrea
31	chr1:225632600-225634600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:225632600-225634800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:225632600-225635400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:225632600-225635400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:225632600-225635800	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr1:225632800-225634000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:225632800-225634000	Enhancers	Osteobl	bone
38	chr1:225632800-225634400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:225632800-225634600	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr1:225632800-225635000	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr1:225632800-225635000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
42	chr1:225632800-225635400	Enhancers	Brain Substantia Nigra	brain
43	chr1:225632800-225636600	Enhancers	Esophagus	oesophagus
44	chr1:225633000-225634000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:225633000-225634000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr1:225633000-225634800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:225633000-225635000	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr1:225633000-225636000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:225633000-225636400	Enhancers	Right Atrium	heart
50	chr1:225633000-225640200	Enhancers	Fetal Thymus	thymus

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