Variant report

Variant	rs9798411
Chromosome Location	chr2:114462197-114462198
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10168234	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10199704	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10200355	0.85[AMR][1000 genomes]
rs10205467	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10206174	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10938	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11679707	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11682259	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11695798	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11897553	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11901060	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12711784	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12711786	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13004622	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13006627	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13029093	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13034531	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13397540	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13405475	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13416930	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1349157	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1584434	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17048473	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2122095	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2305254	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2418915	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35432356	0.82[AMR][1000 genomes]
rs35667749	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4849264	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4849265	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4849266	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4849269	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56213422	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56376185	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58473055	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6542171	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6704673	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6731402	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6739072	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6741521	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67850681	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7561176	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7578249	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7586800	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7587218	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7590375	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7592689	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7600550	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs935644	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[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
rs9798411	DDX11L2	cis	Whole Blood	GTEx
rs9798411	SLC35F5	Cis_1M	lymphoblastoid	RTeQTL
rs9798411	RPL23AP7	Cis_1M	lymphoblastoid	RTeQTL
rs9798411	PS1TP4	Cis_1M	lymphoblastoid	RTeQTL
rs9798411	SLC35F5	cis	Skin Sun Exposed Lower leg	GTEx
rs9798411	RPL23AP7	cis	Muscle Skeletal	GTEx
rs9798411	RPL23AP7	cis	Whole Blood	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114451600-114462400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr2:114452400-114470200	Weak transcription	Primary T cells from cord blood	blood
3	chr2:114452600-114469400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:114453000-114470400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:114455000-114470400	Weak transcription	NHEK	skin
6	chr2:114455400-114472200	Weak transcription	HMEC	breast
7	chr2:114455600-114470400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:114455800-114462400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:114455800-114470400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:114458000-114466400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr2:114458000-114466600	Weak transcription	Primary B cells from cord blood	blood
12	chr2:114458000-114470400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr2:114458000-114472000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr2:114458200-114462200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:114458200-114462400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:114458200-114466600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:114458200-114469600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr2:114458200-114469600	Weak transcription	Adipose Nuclei	Adipose
19	chr2:114458200-114470200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr2:114458200-114470200	Weak transcription	GM12878-XiMat	blood
21	chr2:114458200-114470400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr2:114458200-114470400	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr2:114458200-114470400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:114458200-114486200	Weak transcription	Dnd41	blood
25	chr2:114458200-114512600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr2:114458400-114462400	Weak transcription	Aorta	Aorta
27	chr2:114458400-114463400	Weak transcription	Spleen	Spleen
28	chr2:114458400-114463600	Weak transcription	Left Ventricle	heart
29	chr2:114458400-114467200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:114458400-114469400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:114458400-114469400	Weak transcription	Placenta	Placenta
32	chr2:114458400-114469400	Weak transcription	K562	blood
33	chr2:114458400-114470200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr2:114458400-114470400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:114458400-114470400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:114458400-114470400	Weak transcription	Fetal Thymus	thymus
37	chr2:114458400-114471800	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr2:114458400-114475000	Weak transcription	Thymus	Thymus
39	chr2:114458400-114484200	Weak transcription	Pancreas	Pancrea
40	chr2:114458400-114497200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr2:114458400-114500000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr2:114458800-114469000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:114459600-114463800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:114459800-114462400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:114459800-114462400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:114460000-114462400	Weak transcription	Fetal Muscle Leg	muscle
47	chr2:114460000-114470200	Weak transcription	Fetal Muscle Trunk	muscle
48	chr2:114460000-114470400	Weak transcription	Fetal Brain Female	brain
49	chr2:114460000-114470400	Weak transcription	NHDF-Ad	bronchial
50	chr2:114460200-114462400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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