Variant report

Variant	rs6740044
Chromosome Location	chr2:86227341-86227342
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86227255..86230003-chr2:86232483..86235782,3	K562	blood:
2	chr2:86225886..86228225-chr2:86420684..86422755,2	K562	blood:
3	chr2:86220130..86224322-chr2:86225400..86228402,3	MCF-7	breast:
4	chr2:86226779..86229751-chr2:86239131..86240929,2	K562	blood:

Variant related genes	Relation type
ENSG00000132305	Chromatin interaction
ENSG00000273080	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 16 )

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

rs_ID	r²[population]
rs10175330	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[TSI][hapmap]
rs10178120	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10178540	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10185452	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10187150	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs10198260	0.83[ASN][1000 genomes]
rs10496318	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs1057893	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[TSI][hapmap]
rs11395	0.84[ASW][hapmap];0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap]
rs11885380	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs11899254	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs11900161	0.81[CEU][hapmap]
rs12328100	0.84[ASW][hapmap]
rs12469762	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap]
rs12475079	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs12475126	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs12477274	0.84[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap]
rs12478097	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs12714162	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12714164	0.83[ASN][1000 genomes]
rs12714165	0.83[ASN][1000 genomes]
rs12714166	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12714171	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs12714172	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs12994838	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12996308	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[TSI][hapmap]
rs12997506	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13000793	0.81[CHD][hapmap]
rs13001470	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13004643	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13024123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13027248	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13028023	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs13403186	0.92[CEU][hapmap]
rs1424522	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs17027013	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs2241438	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs2278083	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs2278536	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2288113	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[TSI][hapmap]
rs2288115	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs2289239	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2367203	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[TSI][hapmap]
rs2367204	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs34478066	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34723687	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770062	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs3770065	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs3770067	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs3770075	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3821017	0.89[CEU][hapmap]
rs4374375	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[TSI][hapmap]
rs4402761	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[TSI][hapmap]
rs4422155	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[TSI][hapmap]
rs4450596	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[TSI][hapmap]
rs4544439	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[TSI][hapmap]
rs4597526	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4832018	0.83[ASN][1000 genomes]
rs4832019	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4832020	0.83[ASN][1000 genomes]
rs4832234	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4832236	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6547661	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs6707029	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs6725046	0.81[CEU][hapmap]
rs6725372	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs6729732	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[TSI][hapmap]
rs6731995	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[TSI][hapmap]
rs6735014	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6737950	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs6749090	0.92[CEU][hapmap]
rs6757387	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs715334	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap]
rs735738	1.00[CHB][hapmap]
rs7566721	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs7572386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7588325	0.81[CEU][hapmap]
rs7609008	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[TSI][hapmap]
rs8244	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs876242	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[TSI][hapmap]
rs9309632	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs9309633	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap]
rs9653508	0.92[CEU][hapmap]
rs9653569	1.00[CHB][hapmap]

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	nsv1001104	chr2:86182021-86271923	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv535807	chr2:86182021-86271923	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs6740044	REEP1	cis	parietal	SCAN
rs6740044	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs6740044	IMMT	cis	parietal	SCAN
rs6740044	LOC90784	Cis_1M	lymphoblastoid	RTeQTL
rs6740044	MRPL35	cis	cerebellum	SCAN
rs6740044	IMMT	cis	Esophagus Muscularis	GTEx
rs6740044	ST3GAL5	cis	cerebellum	SCAN
rs6740044	IMMT	cis	lymphoblastoid	seeQTL
rs6740044	IMMT	cis	multi-tissue	Pritchard
rs6740044	IMMT	cis	Whole Blood	GTEx
rs6740044	MRPL35	cis	parietal	SCAN
rs6740044	C2orf51	cis	cerebellum	SCAN
rs6740044	IMMT	cis	Artery Aorta	GTEx
rs6740044	IMMT	Cis_1M	lymphoblastoid	RTeQTL
rs6740044	MRPL35	cis	lymphoblastoid	seeQTL
rs6740044	IMMT	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86219800-86228600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:86219800-86228800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr2:86219800-86229000	Enhancers	Primary B cells from peripheral blood	blood
4	chr2:86219800-86229200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr2:86220400-86227600	Enhancers	Fetal Muscle Trunk	muscle
6	chr2:86220400-86228800	Enhancers	Primary T cells fromperipheralblood	blood
7	chr2:86220800-86227600	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr2:86220800-86228600	Enhancers	Fetal Muscle Leg	muscle
9	chr2:86220800-86228800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr2:86220800-86228800	Enhancers	Fetal Thymus	thymus
11	chr2:86221000-86227400	Enhancers	Lung	lung
12	chr2:86221000-86228400	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr2:86221000-86228600	Enhancers	Primary hematopoietic stem cells	blood
14	chr2:86221000-86228600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr2:86221000-86228600	Enhancers	Spleen	Spleen
16	chr2:86221400-86227600	Enhancers	Brain Cingulate Gyrus	brain
17	chr2:86221400-86228400	Enhancers	Brain Hippocampus Middle	brain
18	chr2:86221400-86228600	Enhancers	Placenta	Placenta
19	chr2:86221600-86228400	Enhancers	Right Atrium	heart
20	chr2:86222600-86228400	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr2:86222600-86228600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:86222600-86229000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr2:86222800-86228400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:86223200-86227400	Enhancers	Left Ventricle	heart
25	chr2:86223400-86227600	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr2:86223400-86228600	Enhancers	Fetal Lung	lung
27	chr2:86223600-86228400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:86223600-86228600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:86223800-86228800	Enhancers	Primary T cells from cord blood	blood
30	chr2:86223800-86228800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr2:86224000-86228600	Enhancers	Fetal Intestine Large	intestine
32	chr2:86224400-86228200	Weak transcription	Esophagus	oesophagus
33	chr2:86224600-86227400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:86225000-86229000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:86225200-86228600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:86225400-86227400	Flanking Active TSS	GM12878-XiMat	blood
37	chr2:86225600-86227800	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr2:86225600-86228400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr2:86225600-86228400	Enhancers	HUVEC	blood vessel
40	chr2:86226000-86228400	Enhancers	NH-A	brain
41	chr2:86226200-86227400	Enhancers	Duodenum Mucosa	Duodenum
42	chr2:86226200-86227600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:86226200-86231800	Enhancers	K562	blood
44	chr2:86226600-86227400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:86226600-86228200	Enhancers	Hela-S3	cervix
46	chr2:86226600-86228200	Enhancers	NHDF-Ad	bronchial
47	chr2:86226600-86228400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:86226800-86227400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr2:86226800-86227600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr2:86226800-86227600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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