Variant report

Variant	rs7585740
Chromosome Location	chr2:231262029-231262030
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10165727	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10181582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10184953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10194531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198517	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11686704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694850	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12694851	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12694853	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12694854	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12694855	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12694856	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12694858	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12694859	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12694860	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12694862	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12694863	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12994857	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13012177	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13012615	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13025664	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13028885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13383901	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13383916	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13383946	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13384148	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13384237	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13384350	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13390006	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13397699	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13409103	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1579395	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1609427	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1820551	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1863672	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1968342	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2894710	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35935297	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3856528	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4364013	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4577270	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4638786	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6709797	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6710190	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6738146	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6738151	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7586155	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9288667	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv875945	chr2:231172642-231267925	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv869708	chr2:231173700-231267616	Genic enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3486129	chr2:231175581-231265831	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv3486131	chr2:231175581-231265831	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2751844	chr2:231179495-231280495	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1006206	chr2:231179884-231268938	Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv875946	chr2:231184106-231277567	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv875947	chr2:231190446-231281286	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7585740	LOC93349	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231212800-231262400	Weak transcription	K562	blood
2	chr2:231220000-231275800	Weak transcription	Stomach Mucosa	stomach
3	chr2:231222200-231273200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr2:231223600-231263600	Weak transcription	Fetal Kidney	kidney
5	chr2:231225200-231268000	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:231228800-231275600	Weak transcription	Psoas Muscle	Psoas
7	chr2:231234200-231274400	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:231237000-231264800	Weak transcription	HepG2	liver
9	chr2:231237200-231264800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:231245200-231265600	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr2:231245800-231266000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:231248000-231262600	Strong transcription	Liver	Liver
13	chr2:231248000-231265400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:231248000-231274600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:231249000-231273200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:231249800-231262600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr2:231250200-231273200	Weak transcription	Right Ventricle	heart
18	chr2:231252600-231272600	Weak transcription	NHDF-Ad	bronchial
19	chr2:231253400-231262600	Strong transcription	Lung	lung
20	chr2:231253600-231262200	Strong transcription	Left Ventricle	heart
21	chr2:231253600-231265800	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:231254000-231264800	Weak transcription	Colonic Mucosa	Colon
23	chr2:231254200-231272800	Weak transcription	NHEK	skin
24	chr2:231254400-231264800	Weak transcription	Gastric	stomach
25	chr2:231254400-231265000	Weak transcription	Pancreas	Pancrea
26	chr2:231254400-231267800	Weak transcription	NHLF	lung
27	chr2:231255200-231275600	Weak transcription	HMEC	breast
28	chr2:231256200-231265000	Weak transcription	HUVEC	blood vessel
29	chr2:231258000-231267600	Weak transcription	Esophagus	oesophagus
30	chr2:231258200-231273000	Weak transcription	NH-A	brain
31	chr2:231258600-231265400	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr2:231258800-231275600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:231259200-231262200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:231259200-231262200	Strong transcription	Osteobl	bone
35	chr2:231259600-231264200	Weak transcription	Fetal Intestine Large	intestine
36	chr2:231259600-231268200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr2:231260000-231265000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:231260200-231275400	Weak transcription	Small Intestine	intestine
39	chr2:231260800-231264200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:231260800-231264600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr2:231260800-231264800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr2:231260800-231265600	Strong transcription	Primary T cells from cord blood	blood
43	chr2:231260800-231272000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr2:231261000-231262600	Strong transcription	Thymus	Thymus
45	chr2:231261000-231262800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:231261000-231262800	Strong transcription	Primary hematopoietic stem cells	blood
47	chr2:231261000-231263000	Strong transcription	Placenta	Placenta
48	chr2:231261000-231263800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr2:231261000-231264200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr2:231261000-231264200	Weak transcription	Spleen	Spleen

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