Variant report

Variant	rs6741521
Chromosome Location	chr2:114476582-114476583
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:114476035..114479420-chr2:114481411..114484659,3	K562	blood:
2	chr2:114470204..114472162-chr2:114473968..114476714,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RABL2A-5	chr2:114475938-114476823	l_1932_chr2:114450946-114476823_testes

Variant related genes	Relation type
ENSG00000115084	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10168234	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10199704	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10200355	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10205467	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10206174	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10938	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11679707	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11682259	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11688799	0.80[ASN][1000 genomes]
rs11695798	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11897553	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11901060	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12711784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12711786	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13004622	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13006627	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13029093	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13034531	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13397540	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13405475	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13416930	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1349157	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1584434	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17048473	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2122095	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305254	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2418915	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35432356	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35667749	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849264	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4849265	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4849266	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4849269	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56213422	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56376185	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58473055	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6542171	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6704673	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6731402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6739072	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67850681	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7561176	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7578249	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7586800	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7587218	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7590375	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7592689	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7600550	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935644	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9798411	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001195	chr2:114362003-114506330	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv979109	chr2:114429638-114495192	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv979339	chr2:114430138-114495192	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1009509	chr2:114432965-114557306	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv535896	chr2:114432965-114557306	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6741521	RPL23AP7	cis	Whole Blood	GTEx
rs6741521	PS1TP4	Cis_1M	lymphoblastoid	RTeQTL
rs6741521	RPL23AP7	Cis_1M	lymphoblastoid	RTeQTL
rs6741521	SLC35F5	Cis_1M	lymphoblastoid	RTeQTL
rs6741521	RPL23AP7	cis	Muscle Skeletal	GTEx
rs6741521	DDX11L2	cis	Whole Blood	GTEx
rs6741521	SLC35F5	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114458200-114486200	Weak transcription	Dnd41	blood
2	chr2:114458200-114512600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:114458400-114484200	Weak transcription	Pancreas	Pancrea
4	chr2:114458400-114497200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr2:114458400-114500000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:114460200-114484200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:114461400-114513200	Weak transcription	Small Intestine	intestine
8	chr2:114461600-114484200	Weak transcription	Lung	lung
9	chr2:114461600-114484400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:114461600-114499800	Weak transcription	Hela-S3	cervix
11	chr2:114462000-114497400	Weak transcription	Colonic Mucosa	Colon
12	chr2:114463000-114498800	Weak transcription	Esophagus	oesophagus
13	chr2:114464000-114484200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:114464000-114484200	Weak transcription	Gastric	stomach
15	chr2:114464000-114497600	Weak transcription	Right Ventricle	heart
16	chr2:114464000-114497600	Weak transcription	Spleen	Spleen
17	chr2:114464600-114484600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr2:114465200-114486400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:114465200-114512000	Weak transcription	Stomach Mucosa	stomach
20	chr2:114465800-114480000	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:114465800-114484800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:114467400-114479800	Weak transcription	Brain Angular Gyrus	brain
23	chr2:114467400-114497200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:114467600-114486200	Weak transcription	Fetal Brain Male	brain
25	chr2:114467800-114484200	Weak transcription	Aorta	Aorta
26	chr2:114468800-114512800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr2:114469400-114477200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:114469400-114477200	Strong transcription	Placenta	Placenta
29	chr2:114469400-114477400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:114469400-114510400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr2:114469600-114476800	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr2:114469800-114482000	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr2:114469800-114486400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr2:114470000-114477400	Strong transcription	Primary B cells from cord blood	blood
35	chr2:114470000-114497400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:114470000-114500200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:114470200-114477200	Strong transcription	Liver	Liver
38	chr2:114470200-114477400	Strong transcription	Primary B cells from peripheral blood	blood
39	chr2:114470200-114477400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:114470200-114493400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:114470200-114511200	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr2:114470400-114477000	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr2:114470400-114477200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:114470400-114477400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:114470400-114477400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:114470400-114510800	Strong transcription	HSMM	muscle
47	chr2:114471000-114480000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:114471000-114483200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:114471000-114486000	Weak transcription	K562	blood
50	chr2:114471000-114488200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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