Variant report

Variant	rs1437614
Chromosome Location	chr2:86726626-86726627
allele	C/T
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	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1030887	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];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11127043	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11548929	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11890032	0.83[EUR][1000 genomes]
rs11891659	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11899532	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1518808	0.93[EUR][1000 genomes]
rs1518810	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs1518812	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17027265	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];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17027270	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17027280	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17027296	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34605051	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs34633268	0.93[EUR][1000 genomes]
rs55688177	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55708352	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55828608	0.93[EUR][1000 genomes]
rs56055358	0.96[EUR][1000 genomes]
rs56085540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56169889	0.93[EUR][1000 genomes]
rs56211578	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56227180	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56242451	0.91[EUR][1000 genomes]
rs56347930	0.93[EUR][1000 genomes]
rs56378606	0.84[EUR][1000 genomes]
rs57291816	0.93[EUR][1000 genomes]
rs57836876	0.96[EUR][1000 genomes]
rs58091125	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58361202	0.93[EUR][1000 genomes]
rs58829418	0.96[EUR][1000 genomes]
rs59026369	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59183618	0.93[EUR][1000 genomes]
rs59255035	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59336972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59521243	0.89[EUR][1000 genomes]
rs59613942	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59859947	0.89[EUR][1000 genomes]
rs59895355	0.89[EUR][1000 genomes]
rs60073472	0.89[EUR][1000 genomes]
rs60244636	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60304516	0.93[EUR][1000 genomes]
rs60717666	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60796561	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60810860	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61028062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61465748	0.89[EUR][1000 genomes]
rs61547860	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6710780	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6720414	0.89[EUR][1000 genomes]
rs6740863	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6745875	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72930315	0.93[EUR][1000 genomes]
rs72930323	0.93[EUR][1000 genomes]
rs72930336	0.93[EUR][1000 genomes]
rs72930340	0.93[EUR][1000 genomes]
rs72930349	0.93[EUR][1000 genomes]
rs72930361	0.93[EUR][1000 genomes]
rs72930362	0.93[EUR][1000 genomes]
rs72930364	0.93[EUR][1000 genomes]
rs72930369	0.93[EUR][1000 genomes]
rs72930387	0.96[EUR][1000 genomes]
rs72930396	0.93[EUR][1000 genomes]
rs72930400	0.93[EUR][1000 genomes]
rs72932307	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72932310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72932311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72932316	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72932319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72932336	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72932350	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72932358	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72932364	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72932369	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72932380	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73949838	0.84[EUR][1000 genomes]
rs73949839	0.84[EUR][1000 genomes]
rs7562493	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7579234	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs7585722	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7586028	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7604179	0.93[EUR][1000 genomes]
rs7608800	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.93[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
rs1437614	MRPL35	cis	parietal	SCAN
rs1437614	KRCC1	cis	cerebellum	SCAN
rs1437614	VPS24	cis	parietal	SCAN
rs1437614	VPS24	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86674200-86726800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:86676600-86727200	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:86681600-86727000	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr2:86696000-86727000	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr2:86697600-86727200	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr2:86697800-86728800	Strong transcription	Primary T cells from cord blood	blood
8	chr2:86699400-86727000	Strong transcription	Placenta	Placenta
9	chr2:86709200-86737400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:86713400-86727400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:86719800-86726800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:86719800-86726800	Strong transcription	Liver	Liver
13	chr2:86719800-86726800	Weak transcription	Esophagus	oesophagus
14	chr2:86719800-86734600	Weak transcription	Psoas Muscle	Psoas
15	chr2:86720400-86727000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:86721400-86728000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
17	chr2:86722000-86727200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:86722200-86727000	Strong transcription	Fetal Stomach	stomach
19	chr2:86722200-86730600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:86723800-86727000	Strong transcription	Fetal Muscle Trunk	muscle
21	chr2:86723800-86728000	Strong transcription	Colon Smooth Muscle	Colon
22	chr2:86724000-86726800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr2:86724000-86727200	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:86724000-86728000	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr2:86724000-86728600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
26	chr2:86724000-86729600	ZNF genes & repeats	GM12878-XiMat	blood
27	chr2:86724200-86726800	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr2:86724200-86727200	Strong transcription	Colonic Mucosa	Colon
29	chr2:86724200-86727400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
30	chr2:86724200-86727400	Strong transcription	Osteobl	bone
31	chr2:86724200-86727600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
32	chr2:86724200-86728600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:86724400-86726800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:86724400-86726800	Strong transcription	Fetal Brain Male	brain
35	chr2:86724400-86727400	Strong transcription	Brain Angular Gyrus	brain
36	chr2:86724400-86728200	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:86724400-86728400	Strong transcription	Left Ventricle	heart
38	chr2:86724400-86729000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
39	chr2:86724600-86728000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
40	chr2:86724600-86728000	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr2:86724600-86728200	ZNF genes & repeats	Dnd41	blood
42	chr2:86724600-86728400	Strong transcription	Rectal Smooth Muscle	rectum
43	chr2:86724600-86737800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr2:86725200-86727200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:86725200-86727400	Strong transcription	Brain Hippocampus Middle	brain
46	chr2:86725200-86727400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:86725200-86729000	Strong transcription	Aorta	Aorta
48	chr2:86725200-86730000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:86725400-86726800	Strong transcription	Brain Substantia Nigra	brain
50	chr2:86725400-86726800	Strong transcription	K562	blood

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