Variant report

Variant	rs6745875
Chromosome Location	chr2:86730470-86730471
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1030886	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1030887	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11127043	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11548929	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11890032	0.89[EUR][1000 genomes]
rs11891659	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11899532	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1437614	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1518808	0.91[EUR][1000 genomes]
rs1518810	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs1518812	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17027265	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17027270	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17027280	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027296	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34605051	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs34633268	0.91[EUR][1000 genomes]
rs55688177	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55708352	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55828608	0.91[EUR][1000 genomes]
rs56055358	0.89[EUR][1000 genomes]
rs56085540	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56169889	0.91[EUR][1000 genomes]
rs56211578	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56227180	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56242451	0.89[EUR][1000 genomes]
rs56347930	0.91[EUR][1000 genomes]
rs56378606	0.90[EUR][1000 genomes]
rs57291816	0.91[EUR][1000 genomes]
rs57836876	0.89[EUR][1000 genomes]
rs58091125	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58361202	0.91[EUR][1000 genomes]
rs58829418	0.89[EUR][1000 genomes]
rs59026369	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59183618	0.87[EUR][1000 genomes]
rs59255035	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59336972	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59521243	0.87[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs59613942	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59859947	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs59895355	0.96[EUR][1000 genomes]
rs60073472	0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs60244636	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60304516	0.91[EUR][1000 genomes]
rs60717666	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60796561	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60810860	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61028062	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61465748	0.96[EUR][1000 genomes]
rs61547860	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6710780	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6720414	0.96[EUR][1000 genomes]
rs6740863	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930315	0.91[EUR][1000 genomes]
rs72930323	0.91[EUR][1000 genomes]
rs72930336	0.91[EUR][1000 genomes]
rs72930340	0.91[EUR][1000 genomes]
rs72930349	0.91[EUR][1000 genomes]
rs72930361	0.91[EUR][1000 genomes]
rs72930362	0.91[EUR][1000 genomes]
rs72930364	0.91[EUR][1000 genomes]
rs72930369	0.91[EUR][1000 genomes]
rs72930387	0.89[EUR][1000 genomes]
rs72930396	0.87[EUR][1000 genomes]
rs72930400	0.87[EUR][1000 genomes]
rs72932307	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72932310	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932311	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932316	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932319	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932350	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932358	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932364	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932369	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932380	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73949838	0.90[EUR][1000 genomes]
rs73949839	0.90[EUR][1000 genomes]
rs7562493	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7579234	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs7585722	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7586028	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7604179	1.00[EUR][1000 genomes]
rs7608800	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6745875	MRPL35	cis	parietal	SCAN
rs6745875	VPS24	Cis_1M	lymphoblastoid	RTeQTL
rs6745875	VPS24	cis	parietal	SCAN
rs6745875	KRCC1	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:86709200-86737400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:86719800-86734600	Weak transcription	Psoas Muscle	Psoas
4	chr2:86722200-86730600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:86724600-86737800	Strong transcription	Stomach Smooth Muscle	stomach
6	chr2:86725400-86733200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:86726000-86731200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:86726400-86735400	Weak transcription	NHLF	lung
9	chr2:86726400-86737400	Weak transcription	HUVEC	blood vessel
10	chr2:86726400-86741800	Weak transcription	NH-A	brain
11	chr2:86726400-86753000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:86726600-86736400	Weak transcription	NHDF-Ad	bronchial
13	chr2:86726600-86748600	Weak transcription	Hela-S3	cervix
14	chr2:86726800-86739000	Weak transcription	K562	blood
15	chr2:86727000-86737200	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr2:86727400-86731000	Weak transcription	Osteobl	bone
17	chr2:86727400-86734400	Weak transcription	Fetal Heart	heart
18	chr2:86727600-86731800	Weak transcription	HSMMtube	muscle
19	chr2:86727600-86732600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:86727600-86734600	Weak transcription	HMEC	breast
21	chr2:86727800-86732000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr2:86728000-86730600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:86728000-86730600	Weak transcription	Colon Smooth Muscle	Colon
24	chr2:86728000-86731000	Weak transcription	Esophagus	oesophagus
25	chr2:86728000-86731000	Weak transcription	Pancreas	Pancrea
26	chr2:86728000-86731800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr2:86728000-86731800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr2:86728000-86732000	Weak transcription	Brain Angular Gyrus	brain
29	chr2:86728000-86732000	Weak transcription	Fetal Kidney	kidney
30	chr2:86728000-86732000	Weak transcription	Gastric	stomach
31	chr2:86728000-86732400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr2:86728000-86732600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr2:86728000-86734200	Weak transcription	HSMM	muscle
34	chr2:86728000-86737600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:86728000-86737600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr2:86728000-86737600	Strong transcription	Adipose Nuclei	Adipose
37	chr2:86728000-86737800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:86728000-86737800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:86728000-86737800	Strong transcription	Fetal Intestine Large	intestine
40	chr2:86728000-86738000	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr2:86728000-86738400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:86728200-86731200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr2:86728200-86731800	Weak transcription	Ovary	ovary
44	chr2:86728200-86737800	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr2:86728200-86737800	Weak transcription	Stomach Mucosa	stomach
46	chr2:86728200-86738400	Strong transcription	Dnd41	blood
47	chr2:86728200-86755800	Weak transcription	Fetal Brain Male	brain
48	chr2:86728400-86731000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:86728400-86731000	Strong transcription	Fetal Lung	lung
50	chr2:86728400-86732000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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