Variant report

Variant	rs2281006
Chromosome Location	chr1:171110869-171110870
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171109416..171111104-chr1:171115194..171116914,2	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10489229	0.82[CHD][hapmap];0.96[ASN][1000 genomes]
rs1080197	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10911841	0.81[LWK][hapmap]
rs11809504	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11812044	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11812061	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12402295	0.84[CHB][hapmap]
rs12403297	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12404455	0.82[EUR][1000 genomes]
rs12405599	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12406572	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17564980	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17565336	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17565579	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17565766	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17565793	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17565983	0.98[ASN][1000 genomes]
rs17565990	0.83[ASN][1000 genomes]
rs17566256	0.96[ASN][1000 genomes]
rs17623477	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17623598	0.98[ASN][1000 genomes]
rs17623833	0.96[ASN][1000 genomes]
rs17640463	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.96[ASN][1000 genomes]
rs2066529	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2142630	0.86[ASN][1000 genomes]
rs2266780	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2272797	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.96[ASN][1000 genomes]
rs2272799	0.96[ASN][1000 genomes]
rs2272800	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.85[MEX][hapmap];0.96[ASN][1000 genomes]
rs2281007	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281008	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28363530	0.82[EUR][1000 genomes]
rs28363536	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28363537	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28363541	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28363571	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35156637	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3817765	0.96[ASN][1000 genomes]
rs55639094	0.97[ASN][1000 genomes]
rs57147275	0.96[ASN][1000 genomes]
rs57519348	0.96[ASN][1000 genomes]
rs57678907	0.96[ASN][1000 genomes]
rs58044560	0.96[ASN][1000 genomes]
rs58374074	0.96[ASN][1000 genomes]
rs58509777	0.96[ASN][1000 genomes]
rs59184216	0.96[ASN][1000 genomes]
rs6608452	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6608453	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6608454	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7051747	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7054839	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7061710	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7063044	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7066454	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72712649	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72712658	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72712685	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7879557	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7885569	0.96[ASN][1000 genomes]
rs7886938	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.85[MEX][hapmap];0.96[ASN][1000 genomes]
rs7887142	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.85[MEX][hapmap];0.96[ASN][1000 genomes]
rs7889807	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7889839	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.85[MEX][hapmap];0.96[ASN][1000 genomes]
rs909531	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2281006	RP1-127D3.4	cis	Adipose Subcutaneous	GTEx
rs2281006	FMO2	cis	Adipose Subcutaneous	GTEx
rs2281006	FMO2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171105400-171111200	Weak transcription	Aorta	Aorta
2	chr1:171107200-171111200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:171107200-171111200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:171107200-171111400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:171107200-171111400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:171107800-171112400	Enhancers	Fetal Muscle Leg	muscle
7	chr1:171108000-171112600	Weak transcription	Small Intestine	intestine
8	chr1:171108400-171112800	Enhancers	NHLF	lung
9	chr1:171108800-171111000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr1:171108800-171112400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:171108800-171112800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr1:171109000-171111200	Enhancers	Fetal Intestine Small	intestine
13	chr1:171109000-171112200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:171109000-171112200	Enhancers	Stomach Mucosa	stomach
15	chr1:171109200-171111000	Enhancers	Fetal Intestine Large	intestine
16	chr1:171109200-171112000	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr1:171109200-171112200	Weak transcription	Psoas Muscle	Psoas
18	chr1:171109200-171112400	Enhancers	Fetal Stomach	stomach
19	chr1:171109400-171111000	Enhancers	Liver	Liver
20	chr1:171109400-171111200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:171109400-171112000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:171109400-171112800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr1:171109600-171111200	Enhancers	Fetal Heart	heart
24	chr1:171109800-171111800	Weak transcription	Brain Angular Gyrus	brain
25	chr1:171110000-171111000	Weak transcription	Ovary	ovary
26	chr1:171110200-171111200	Enhancers	Muscle Satellite Cultured Cells	--
27	chr1:171110200-171111200	Enhancers	Brain Cingulate Gyrus	brain
28	chr1:171110200-171111200	Enhancers	NHDF-Ad	bronchial
29	chr1:171110200-171111600	Enhancers	Brain Hippocampus Middle	brain
30	chr1:171110200-171112200	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr1:171110200-171112400	Enhancers	Osteobl	bone
32	chr1:171110400-171111000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:171110400-171111200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:171110400-171112000	Enhancers	HSMMtube	muscle
35	chr1:171110400-171112000	Enhancers	NH-A	brain
36	chr1:171110400-171112200	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr1:171110600-171111000	Enhancers	Adipose Nuclei	Adipose
38	chr1:171110600-171111400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:171110600-171111400	Enhancers	Left Ventricle	heart
40	chr1:171110600-171111600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:171110600-171112400	Enhancers	HepG2	liver
42	chr1:171110800-171111000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:171110800-171111000	Weak transcription	Colon Smooth Muscle	Colon
44	chr1:171110800-171111200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:171110800-171111400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:171110800-171111400	Enhancers	Fetal Muscle Trunk	muscle
47	chr1:171110800-171111800	Weak transcription	Fetal Kidney	kidney
48	chr1:171110800-171112000	Weak transcription	Right Atrium	heart
49	chr1:171110800-171112400	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr1:171110800-171114600	Enhancers	Fetal Lung	lung

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