Variant report

Variant	rs6735090
Chromosome Location	chr2:11425110-11425111
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11425026..11427134-chr2:11483302..11485357,2	K562	blood:
2	chr2:11420942..11423564-chr2:11424238..11426360,2	K562	blood:
3	chr2:11422735..11425372-chr2:11448792..11450664,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134318	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10168440	0.91[AFR][1000 genomes]
rs10169455	0.85[AMR][1000 genomes]
rs10175719	0.83[AMR][1000 genomes]
rs10178332	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10183296	0.90[AMR][1000 genomes]
rs10192994	0.90[AMR][1000 genomes]
rs10194620	0.90[AMR][1000 genomes]
rs10203916	0.86[AMR][1000 genomes]
rs10206334	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10210600	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10454126	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10754957	0.89[EUR][1000 genomes]
rs10929730	0.87[EUR][1000 genomes]
rs11681822	0.86[AMR][1000 genomes]
rs11694729	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11695377	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12692434	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12692437	0.84[AMR][1000 genomes]
rs12994807	0.81[AMR][1000 genomes]
rs13002722	0.85[AMR][1000 genomes]
rs13014721	0.83[AMR][1000 genomes]
rs1515224	0.93[EUR][1000 genomes]
rs1562748	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1562749	0.92[EUR][1000 genomes]
rs2044758	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2060635	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2084577	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2100228	0.94[EUR][1000 genomes]
rs2122384	0.81[AMR][1000 genomes]
rs2167126	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2357995	0.85[AMR][1000 genomes]
rs2357996	0.92[EUR][1000 genomes]
rs3911110	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4303693	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4353615	0.83[AMR][1000 genomes]
rs4668720	0.81[AMR][1000 genomes]
rs4669699	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4669701	0.86[AMR][1000 genomes]
rs4669706	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4669709	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4669710	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4669711	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4669712	0.84[AMR][1000 genomes]
rs4669713	0.84[AMR][1000 genomes]
rs62118012	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6432183	0.92[EUR][1000 genomes]
rs6432185	0.81[AMR][1000 genomes]
rs6432186	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6706126	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6710031	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6713273	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6713382	0.90[AMR][1000 genomes]
rs6721445	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6732258	0.81[AMR][1000 genomes]
rs6733312	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6736240	0.81[AMR][1000 genomes]
rs6749456	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6753875	0.89[AMR][1000 genomes]
rs6755196	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6760802	0.93[EUR][1000 genomes]
rs7355446	0.86[AMR][1000 genomes]
rs753770	0.86[AMR][1000 genomes]
rs7558664	0.83[AMR][1000 genomes]
rs7563468	0.89[AMR][1000 genomes]
rs7563928	0.86[AMR][1000 genomes]
rs7573458	0.94[EUR][1000 genomes]
rs7575837	0.81[AMR][1000 genomes]
rs7593091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9287728	0.92[EUR][1000 genomes]
rs965665	0.93[EUR][1000 genomes]
rs9712182	0.81[AMR][1000 genomes]
rs9808228	0.92[EUR][1000 genomes]
rs9967898	0.92[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
rs6735090	PQLC3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11310600-11433000	Weak transcription	Pancreas	Pancrea
2	chr2:11361200-11425600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:11378800-11428600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:11394800-11432800	Weak transcription	Right Ventricle	heart
5	chr2:11410400-11433000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr2:11410800-11432800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:11411200-11432800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr2:11411400-11426400	Weak transcription	Gastric	stomach
9	chr2:11413000-11427400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:11413000-11427800	Weak transcription	Aorta	Aorta
11	chr2:11413000-11431400	Weak transcription	Lung	lung
12	chr2:11415400-11428800	Strong transcription	HepG2	liver
13	chr2:11415600-11428600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:11416200-11426400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:11416200-11428000	Weak transcription	Stomach Mucosa	stomach
16	chr2:11418000-11431000	Weak transcription	Psoas Muscle	Psoas
17	chr2:11418800-11428400	Weak transcription	NHLF	lung
18	chr2:11420800-11430400	Weak transcription	Small Intestine	intestine
19	chr2:11420800-11433000	Weak transcription	Spleen	Spleen
20	chr2:11421000-11426600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:11421600-11425600	Weak transcription	K562	blood
22	chr2:11422200-11427800	Weak transcription	HUVEC	blood vessel
23	chr2:11422800-11427200	Strong transcription	Fetal Intestine Large	intestine
24	chr2:11423000-11425200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:11423200-11426000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:11423600-11426000	Weak transcription	Esophagus	oesophagus
27	chr2:11423600-11426600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:11423800-11425200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
29	chr2:11423800-11425800	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr2:11423800-11425800	Strong transcription	Osteobl	bone
31	chr2:11423800-11426000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:11423800-11426000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:11423800-11426000	ZNF genes & repeats	Dnd41	blood
34	chr2:11423800-11426200	Strong transcription	Fetal Thymus	thymus
35	chr2:11423800-11426200	Strong transcription	HSMM	muscle
36	chr2:11423800-11426600	Strong transcription	Primary T cells from cord blood	blood
37	chr2:11423800-11426600	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr2:11423800-11426600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:11423800-11426600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:11423800-11426600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:11423800-11426600	Strong transcription	Placenta	Placenta
42	chr2:11423800-11426600	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr2:11423800-11426600	ZNF genes & repeats	GM12878-XiMat	blood
44	chr2:11423800-11426800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:11423800-11427200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:11423800-11427200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr2:11423800-11427200	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr2:11424000-11426000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr2:11424000-11426000	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr2:11424000-11426000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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