Variant report

Variant	rs62248580
Chromosome Location	chr3:47439291-47439292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1038394	0.88[EUR][1000 genomes]
rs10865946	0.90[EUR][1000 genomes]
rs11130127	0.81[EUR][1000 genomes]
rs11130129	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs11705957	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11711824	0.87[EUR][1000 genomes]
rs11712445	0.90[EUR][1000 genomes]
rs11719877	0.90[EUR][1000 genomes]
rs11925823	0.90[EUR][1000 genomes]
rs12486969	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12487736	0.81[EUR][1000 genomes]
rs12497225	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12632132	0.81[EUR][1000 genomes]
rs12636851	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13064843	0.90[EUR][1000 genomes]
rs13075233	0.90[EUR][1000 genomes]
rs13079098	0.91[EUR][1000 genomes]
rs1531875	0.89[EUR][1000 genomes]
rs17410853	0.81[AMR][1000 genomes]
rs17411375	0.81[EUR][1000 genomes]
rs1872164	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2062278	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2101247	0.80[EUR][1000 genomes]
rs2159400	0.80[EUR][1000 genomes]
rs3736177	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4241548	0.86[EUR][1000 genomes]
rs4858805	0.89[EUR][1000 genomes]
rs4858848	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4858868	0.88[EUR][1000 genomes]
rs4858888	0.82[EUR][1000 genomes]
rs553989	0.80[EUR][1000 genomes]
rs56032309	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs56351005	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs57346147	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs60369822	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62246474	0.81[EUR][1000 genomes]
rs6780013	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6787422	0.90[EUR][1000 genomes]
rs6792461	0.87[EUR][1000 genomes]
rs6800271	0.87[EUR][1000 genomes]
rs7613282	0.80[EUR][1000 genomes]
rs7641010	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7651762	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs807810	0.82[EUR][1000 genomes]
rs878659	0.80[EUR][1000 genomes]
rs922957	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	esv1807553	chr3:47393616-47470763	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv3802	chr3:47396674-47441951	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Enhancers 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	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62248580	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs62248580	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47423600-47446000	Weak transcription	Colonic Mucosa	Colon
2	chr3:47423800-47447400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:47423800-47448000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:47423800-47449800	Weak transcription	A549	lung
5	chr3:47424000-47446000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:47426200-47462400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:47427600-47448400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr3:47428200-47449000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:47430200-47449600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:47431000-47448600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:47434000-47447400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:47435600-47440600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:47435600-47441800	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:47435800-47440200	Strong transcription	Primary B cells from cord blood	blood
15	chr3:47435800-47442000	Strong transcription	Primary T cells from cord blood	blood
16	chr3:47436000-47442000	Strong transcription	Fetal Intestine Large	intestine
17	chr3:47436000-47446200	Strong transcription	Fetal Intestine Small	intestine
18	chr3:47436000-47454600	Weak transcription	Hela-S3	cervix
19	chr3:47436200-47442000	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr3:47436200-47462000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr3:47436400-47440400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:47436400-47441800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:47436400-47442000	Strong transcription	Primary hematopoietic stem cells	blood
24	chr3:47436400-47442000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:47436400-47442000	Strong transcription	Thymus	Thymus
26	chr3:47436400-47443600	Strong transcription	Dnd41	blood
27	chr3:47436400-47446000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:47436400-47446000	Strong transcription	Fetal Stomach	stomach
29	chr3:47436600-47440400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr3:47436600-47442000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:47436600-47442000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr3:47436600-47446000	Weak transcription	Stomach Mucosa	stomach
33	chr3:47436600-47447800	Weak transcription	Small Intestine	intestine
34	chr3:47436600-47454800	Weak transcription	Fetal Kidney	kidney
35	chr3:47436800-47439400	Strong transcription	Primary B cells from peripheral blood	blood
36	chr3:47436800-47440200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:47436800-47441400	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:47436800-47442000	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr3:47436800-47446200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:47436800-47447800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr3:47437000-47440600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:47437000-47440600	Weak transcription	NH-A	brain
43	chr3:47437000-47443600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr3:47437000-47444200	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:47437000-47446000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:47437000-47448200	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr3:47437000-47450000	Weak transcription	HUVEC	blood vessel
48	chr3:47437200-47439400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:47437200-47439600	Weak transcription	Lung	lung
50	chr3:47437200-47440400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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