Variant report

Variant	rs4402119
Chromosome Location	chr1:223689014-223689015
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223686710..223689558-chr1:223691137..223693488,3	K562	blood:
2	chr1:223678801..223680634-chr1:223687720..223690003,2	K562	blood:
3	chr1:223682735..223685673-chr1:223687995..223689647,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11261301	0.85[AFR][1000 genomes]
rs12124770	0.85[AFR][1000 genomes]
rs12136518	0.87[ASN][1000 genomes]
rs12403119	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12408545	0.93[ASN][1000 genomes]
rs12409225	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12411081	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12732440	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12735811	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12752130	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12760595	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17162209	0.86[AFR][1000 genomes]
rs34285879	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34766468	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35219153	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36046682	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3935463	0.87[ASN][1000 genomes]
rs4353087	0.97[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4421579	0.85[AFR][1000 genomes]
rs4606305	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55939627	0.93[ASN][1000 genomes]
rs56170942	0.96[ASN][1000 genomes]
rs56296308	0.96[ASN][1000 genomes]
rs59248273	0.96[ASN][1000 genomes]
rs61366469	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6604718	0.89[ASN][1000 genomes]
rs6604721	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6660728	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6667089	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6676169	0.86[ASN][1000 genomes]
rs6676669	0.96[ASN][1000 genomes]
rs6684384	0.83[ASN][1000 genomes]
rs6685101	0.85[AFR][1000 genomes]
rs72745975	0.96[ASN][1000 genomes]
rs72745981	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7517145	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7549968	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520420	chr1:223682051-223693162	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4402119	BPNT1	cis	parietal	SCAN
rs4402119	HHIPL2	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223685800-223690400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:223685800-223690600	Enhancers	Primary T cells fromperipheralblood	blood
3	chr1:223686000-223689200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:223686200-223691200	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr1:223686600-223690400	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr1:223686800-223690400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:223686800-223690400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr1:223686800-223691200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:223687000-223690200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:223687000-223690400	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr1:223687400-223689600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr1:223687400-223690000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr1:223687600-223689400	Bivalent Enhancer	Dnd41	blood
14	chr1:223687600-223690200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:223687800-223689200	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr1:223687800-223689400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:223688600-223689600	Weak transcription	Pancreas	Pancrea
18	chr1:223688600-223690600	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr1:223688800-223689200	Weak transcription	Fetal Thymus	thymus
20	chr1:223688800-223689400	Enhancers	NHEK	skin
21	chr1:223688800-223689800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:223688800-223690000	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr1:223689000-223689800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:223689000-223689800	Enhancers	HMEC	breast

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