Variant report

Variant	rs28378040
Chromosome Location	chr2:30666831-30666832
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:30659808..30662413-chr2:30664986..30667717,2	K562	blood:
2	chr2:30665155..30667715-chr2:30668853..30672910,4	K562	blood:
3	chr2:30665529..30667987-chr2:30668853..30670982,3	K562	blood:
4	chr2:30666695..30668837-chr2:30882273..30884825,2	K562	blood:
5	chr2:30662772..30665115-chr2:30666031..30669960,4	K562	blood:
6	chr2:30666329..30668432-chr2:30685565..30687906,2	K562	blood:

Variant related genes	Relation type
ENSG00000172954	Chromatin interaction

Extended variants
information (count: 149 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs10169001	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10169512	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170012	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10174170	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10176138	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10178307	0.84[EUR][1000 genomes]
rs10178829	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180054	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181161	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10186917	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10197915	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10198587	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200895	0.84[EUR][1000 genomes]
rs10201020	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10204301	0.90[EUR][1000 genomes]
rs10206659	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10206668	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10208299	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208587	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210365	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10211659	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10514772	0.84[EUR][1000 genomes]
rs1074066	0.84[EUR][1000 genomes]
rs11127277	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11127279	0.90[EUR][1000 genomes]
rs11885407	0.87[EUR][1000 genomes]
rs11886181	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11896768	0.84[EUR][1000 genomes]
rs11899182	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11901989	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903573	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12463548	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12465894	0.85[EUR][1000 genomes]
rs12466071	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12467017	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12467830	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12467831	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12468971	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12469630	0.84[EUR][1000 genomes]
rs12469745	0.84[EUR][1000 genomes]
rs12469849	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471248	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12474202	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12475104	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12476387	0.90[EUR][1000 genomes]
rs12476392	0.90[EUR][1000 genomes]
rs12476805	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12477267	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12478778	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13382540	0.90[ASN][1000 genomes]
rs13383939	0.84[EUR][1000 genomes]
rs13388031	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13388156	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13388701	0.83[EUR][1000 genomes]
rs13389142	0.84[EUR][1000 genomes]
rs13390344	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13391492	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13393150	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13397800	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13398796	0.84[EUR][1000 genomes]
rs13401246	0.88[EUR][1000 genomes]
rs13404307	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13412012	0.90[EUR][1000 genomes]
rs13413678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13413980	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13414468	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13417949	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13419209	0.83[EUR][1000 genomes]
rs13419435	0.83[EUR][1000 genomes]
rs13422024	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13424441	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13427862	0.84[EUR][1000 genomes]
rs13428342	0.84[EUR][1000 genomes]
rs13430515	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430622	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430781	0.84[EUR][1000 genomes]
rs13432085	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1404607	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17009601	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17009805	0.87[EUR][1000 genomes]
rs17009808	0.90[EUR][1000 genomes]
rs1869425	0.84[EUR][1000 genomes]
rs1869426	0.84[EUR][1000 genomes]
rs1880539	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1880541	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1982286	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1997036	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997037	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028668	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2077985	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2084301	0.84[EUR][1000 genomes]
rs2100112	0.83[EUR][1000 genomes]
rs2100113	0.84[EUR][1000 genomes]
rs2123757	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2166669	0.83[EUR][1000 genomes]
rs2167970	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2363291	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2363294	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2363311	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2363851	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4144806	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4951991	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4951993	0.86[EUR][1000 genomes]
rs4951994	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4951995	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4951996	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4951997	0.84[EUR][1000 genomes]
rs4951998	0.84[EUR][1000 genomes]
rs4952000	0.83[EUR][1000 genomes]
rs4952126	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952127	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4952128	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952129	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952130	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952131	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952132	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4952133	0.85[AMR][1000 genomes]
rs4952135	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4952136	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4952137	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4952139	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4952141	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4952142	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4952143	0.81[ASN][1000 genomes]
rs4952145	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4952146	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4952149	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4952150	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4952152	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4952154	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4952155	0.87[EUR][1000 genomes]
rs4952158	0.84[EUR][1000 genomes]
rs4952159	0.83[EUR][1000 genomes]
rs4952161	0.84[EUR][1000 genomes]
rs4952162	0.84[EUR][1000 genomes]
rs4952163	0.84[EUR][1000 genomes]
rs4952164	0.84[EUR][1000 genomes]
rs55789733	0.87[EUR][1000 genomes]
rs6739248	0.84[EUR][1000 genomes]
rs7355326	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7355456	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7597579	0.84[EUR][1000 genomes]
rs7603834	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7603947	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7605131	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs766880	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9309681	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv833648	chr2:30505882-30696275	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28378040	LYCAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30661600-30669400	Weak transcription	Primary B cells from cord blood	blood
2	chr2:30663000-30669400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:30663200-30669400	Weak transcription	Thymus	Thymus
4	chr2:30663200-30669600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:30663600-30669000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr2:30663600-30669000	Weak transcription	Fetal Heart	heart
7	chr2:30663600-30669400	Weak transcription	Primary T cells from cord blood	blood
8	chr2:30663800-30669400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr2:30666000-30667600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:30666200-30667000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:30666200-30668800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:30666600-30667600	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr2:30666600-30668600	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr2:30666600-30668600	Enhancers	Adipose Nuclei	Adipose
15	chr2:30666600-30669400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:30666600-30669400	Weak transcription	A549	lung
17	chr2:30666800-30667800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr2:30666800-30669400	Weak transcription	K562	blood
19	chr2:30666800-30669800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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