Variant report

Variant	rs10206334
Chromosome Location	chr2:11419215-11419216
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10168440	0.92[AFR][1000 genomes]
rs10169455	0.89[AMR][1000 genomes]
rs10175719	0.87[AMR][1000 genomes]
rs10178332	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10183296	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10192593	0.83[AMR][1000 genomes]
rs10192994	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10194620	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10203916	0.82[AMR][1000 genomes]
rs10210600	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10454126	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10754957	0.92[EUR][1000 genomes]
rs10929730	0.84[EUR][1000 genomes]
rs11681822	0.82[AMR][1000 genomes]
rs11694729	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11695377	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12477052	0.81[AMR][1000 genomes]
rs12692434	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13002722	0.89[AMR][1000 genomes]
rs1515224	0.96[EUR][1000 genomes]
rs1562748	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1562749	0.94[EUR][1000 genomes]
rs2044758	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2060635	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2084577	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2100228	0.97[EUR][1000 genomes]
rs2167126	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2357995	0.89[AMR][1000 genomes]
rs2357996	0.94[EUR][1000 genomes]
rs3911110	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4303693	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4353615	0.87[AMR][1000 genomes]
rs4668720	0.85[AMR][1000 genomes]
rs4669699	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4669701	0.86[AMR][1000 genomes]
rs4669706	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4669709	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4669710	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4669711	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62118012	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6432183	0.94[EUR][1000 genomes]
rs6432186	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6706126	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6710031	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6713273	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6713382	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6721445	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6730673	0.83[AMR][1000 genomes]
rs6733312	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6735090	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6749456	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6753875	0.85[AMR][1000 genomes]
rs6755196	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6760802	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7355446	0.82[AMR][1000 genomes]
rs753770	0.82[AMR][1000 genomes]
rs7558664	0.87[AMR][1000 genomes]
rs7563468	0.85[AMR][1000 genomes]
rs7563928	0.82[AMR][1000 genomes]
rs7568064	0.83[AMR][1000 genomes]
rs7573458	0.92[EUR][1000 genomes]
rs7593091	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7593966	0.80[AMR][1000 genomes]
rs9287728	0.94[EUR][1000 genomes]
rs965665	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9808228	0.94[EUR][1000 genomes]
rs9967898	0.94[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	esv3395022	chr2:11316915-11426380	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv526038	chr2:11369078-11489531	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	esv1827245	chr2:11385834-11442583	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10206334	PQLC3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11310600-11433000	Weak transcription	Pancreas	Pancrea
2	chr2:11352800-11424000	Weak transcription	HSMMtube	muscle
3	chr2:11354600-11423800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:11361200-11425600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:11364400-11423800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr2:11372600-11423800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:11378800-11428600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:11383000-11424000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:11389800-11423800	Weak transcription	Colonic Mucosa	Colon
10	chr2:11391400-11423800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:11391400-11423800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr2:11391400-11423800	Weak transcription	Ovary	ovary
13	chr2:11391600-11424000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:11391600-11424000	Weak transcription	NHEK	skin
15	chr2:11392400-11423800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:11394800-11420400	Weak transcription	Small Intestine	intestine
17	chr2:11394800-11423800	Weak transcription	Fetal Kidney	kidney
18	chr2:11394800-11432800	Weak transcription	Right Ventricle	heart
19	chr2:11396600-11423800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:11397600-11423200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr2:11404400-11423800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:11404400-11423800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr2:11404600-11423800	Weak transcription	Colon Smooth Muscle	Colon
24	chr2:11404800-11423800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr2:11404800-11423800	Weak transcription	Fetal Heart	heart
26	chr2:11406200-11423800	Weak transcription	Fetal Brain Female	brain
27	chr2:11409000-11424000	Weak transcription	Fetal Brain Male	brain
28	chr2:11409400-11423800	Weak transcription	NH-A	brain
29	chr2:11409800-11423800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:11409800-11424200	Weak transcription	HMEC	breast
31	chr2:11410200-11423000	Weak transcription	Fetal Intestine Small	intestine
32	chr2:11410400-11433000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr2:11410800-11432800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:11411200-11432800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:11411400-11423800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr2:11411400-11426400	Weak transcription	Gastric	stomach
37	chr2:11411600-11423000	Weak transcription	Fetal Stomach	stomach
38	chr2:11411600-11423600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr2:11411600-11423800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr2:11411800-11420800	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr2:11411800-11423200	Weak transcription	Fetal Muscle Leg	muscle
42	chr2:11411800-11423800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr2:11411800-11423800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr2:11411800-11423800	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr2:11411800-11423800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr2:11411800-11423800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr2:11411800-11423800	Weak transcription	Fetal Thymus	thymus
48	chr2:11411800-11424000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr2:11412000-11424200	Weak transcription	Thymus	Thymus
50	chr2:11412200-11424400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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