Variant report

Variant	rs225298
Chromosome Location	chr17:33923946-33923947
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	chr17:33922858..33924678-chr17:34135851..34137902,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PEX12-1	chr17:33923923-33924147	NONHSAT053112

Variant related genes	Relation type
ENSG00000267578	Chromatin interaction
ENSG00000172660	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10438814	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1080352	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11080356	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11652234	1.00[ASN][1000 genomes]
rs1634683	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17550632	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17550716	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17638867	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs178736	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs188959	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2011528	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2011897	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225244	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225246	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225248	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225249	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225250	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225252	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225256	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225257	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225258	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225260	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225261	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225264	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225265	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225266	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225267	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225268	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225270	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225271	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225274	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225275	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225276	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225278	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225279	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225283	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225285	0.95[ASN][1000 genomes]
rs225286	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225287	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225288	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225289	0.81[EUR][1000 genomes]
rs225292	0.89[EUR][1000 genomes]
rs225294	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225296	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225300	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225303	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225305	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225307	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225308	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226084	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs226087	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs226089	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs226090	0.95[EUR][1000 genomes]
rs2376177	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2428464	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2523114	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2523116	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2523117	0.86[EUR][1000 genomes]
rs2626625	0.95[EUR][1000 genomes]
rs2626626	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35542792	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3859282	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3859284	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3890900	0.87[EUR][1000 genomes]
rs4795086	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4796098	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4796100	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4796101	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4796104	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58394103	0.91[AFR][1000 genomes]
rs6505484	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6505485	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6505486	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6505487	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7208672	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7210966	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7211724	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7213804	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7214250	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7214742	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7217378	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7217533	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7221203	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72828038	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72829922	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72829923	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72829925	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72829927	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72829932	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72829933	0.86[EUR][1000 genomes]
rs72829936	0.80[EUR][1000 genomes]
rs72829940	0.81[EUR][1000 genomes]
rs7405825	0.91[ASN][1000 genomes]
rs8064895	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8071584	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8072676	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8074800	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8077826	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9303690	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9649	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9912939	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
2	nsv908079	chr17:33849869-34034851	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv1060890	chr17:33884124-34011034	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv543318	chr17:33884124-34011034	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs225298	LOC645744	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33915200-33930600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:33915200-33932600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:33915600-33954600	Weak transcription	Small Intestine	intestine
4	chr17:33916000-33942000	Weak transcription	Right Atrium	heart
5	chr17:33916400-33924200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr17:33916400-33944800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr17:33916800-33924600	Weak transcription	Brain Substantia Nigra	brain
8	chr17:33916800-33925200	Weak transcription	Fetal Brain Male	brain
9	chr17:33916800-33925200	Weak transcription	Fetal Kidney	kidney
10	chr17:33916800-33945400	Weak transcription	Stomach Mucosa	stomach
11	chr17:33916800-34001200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr17:33917600-33934600	Weak transcription	Brain Angular Gyrus	brain
13	chr17:33919400-33940000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr17:33919600-33931000	Strong transcription	K562	blood
15	chr17:33920000-33937400	Strong transcription	A549	lung
16	chr17:33920400-33936400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr17:33920600-33926600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr17:33920600-33939800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr17:33920600-33939800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr17:33920600-33939800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr17:33920600-33940000	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr17:33920600-33940200	Strong transcription	Primary B cells from peripheral blood	blood
23	chr17:33920600-33942200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr17:33920600-33942800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr17:33920600-33944000	Strong transcription	Dnd41	blood
26	chr17:33920600-33969800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr17:33920800-33926200	Strong transcription	Primary B cells from cord blood	blood
28	chr17:33920800-33931000	Strong transcription	GM12878-XiMat	blood
29	chr17:33920800-33931000	Strong transcription	Osteobl	bone
30	chr17:33920800-33938400	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr17:33920800-33975800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr17:33921000-33925800	Strong transcription	Hela-S3	cervix
33	chr17:33921000-33926600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr17:33921000-33926800	Strong transcription	HMEC	breast
35	chr17:33921000-33930600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr17:33921000-33930800	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr17:33921000-33930800	Strong transcription	NH-A	brain
38	chr17:33921000-33931400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr17:33921000-33931600	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr17:33921000-33932000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr17:33921000-33937200	Strong transcription	Placenta	Placenta
42	chr17:33921000-33939800	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr17:33921000-33939800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr17:33921000-33940400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr17:33921000-33941400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr17:33921000-33942200	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr17:33921000-33943000	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr17:33921000-33946200	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr17:33921000-33946600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr17:33921000-34024400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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