Variant report

Variant	rs3749117
Chromosome Location	chr2:160885442-160885443
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:160883421..160886605-chr2:160893370..160896450,3	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10497205	1.00[YRI][hapmap]
rs10497209	1.00[YRI][hapmap]
rs10497210	1.00[YRI][hapmap]
rs10497213	0.86[JPT][hapmap]
rs10929965	0.85[CHD][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs13001911	0.81[JPT][hapmap]
rs16844715	1.00[YRI][hapmap]
rs16844848	0.81[JPT][hapmap]
rs16844863	0.81[JPT][hapmap]
rs16844866	0.81[JPT][hapmap]
rs17216980	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs17218566	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs17231342	1.00[YRI][hapmap]
rs17231993	1.00[YRI][hapmap]
rs17241282	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17341301	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs17828159	1.00[YRI][hapmap]
rs17829873	1.00[YRI][hapmap]
rs17830307	1.00[YRI][hapmap]
rs17830558	1.00[YRI][hapmap]
rs17830755	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17830904	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17830940	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17831161	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs17831191	0.83[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs17831251	0.83[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs2124969	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs2175416	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2198918	0.81[JPT][hapmap]
rs2221808	1.00[YRI][hapmap]
rs2305818	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs2305819	0.85[JPT][hapmap]
rs35771982	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749114	1.00[YRI][hapmap]
rs3749119	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs3792168	1.00[YRI][hapmap]
rs3792175	1.00[YRI][hapmap]
rs3792192	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3828324	1.00[YRI][hapmap]
rs4292050	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs4664308	0.83[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs4665138	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4665140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4665141	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4665147	0.83[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs4665161	0.81[JPT][hapmap]
rs4665162	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs55668231	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59137532	0.93[ASN][1000 genomes]
rs62175487	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62175488	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66484345	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66667042	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6705574	0.89[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6707458	0.83[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs6719686	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs6722275	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6731260	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs6732107	0.81[JPT][hapmap]
rs6739867	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs6759836	0.83[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs6759924	1.00[YRI][hapmap]
rs877200	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs877635	0.80[TSI][hapmap]
rs925410	0.83[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs979129	1.00[YRI][hapmap]
rs983916	1.00[YRI][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	nsv875345	chr2:160805582-160885442	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv2997	chr2:160841578-160886352	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3749117	LY75	cis	Esophagus Mucosa	GTEx
rs3749117	LY75	cis	cerebellum	SCAN
rs3749117	LY75	cis	lung	GTEx
rs3749117	LY75	cis	Thyroid	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:160828600-160907200	Weak transcription	Small Intestine	intestine
2	chr2:160862800-160899600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:160867600-160893800	Weak transcription	HMEC	breast
4	chr2:160876800-160895800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:160879400-160908000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:160879600-160887800	Weak transcription	NHDF-Ad	bronchial
7	chr2:160879800-160889400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:160879800-160896200	Weak transcription	Colon Smooth Muscle	Colon
9	chr2:160879800-160907800	Weak transcription	NHEK	skin
10	chr2:160881200-160912000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:160881200-160913400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:160881400-160885800	Weak transcription	Gastric	stomach
13	chr2:160881600-160898400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:160881600-160900800	Weak transcription	Spleen	Spleen
15	chr2:160881600-160902000	Weak transcription	Esophagus	oesophagus
16	chr2:160883000-160893600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr2:160883600-160891000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:160883800-160885600	Weak transcription	Aorta	Aorta
19	chr2:160884000-160911600	Weak transcription	Fetal Kidney	kidney
20	chr2:160884600-160885600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:160884600-160885800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:160884600-160885800	Enhancers	Adipose Nuclei	Adipose
23	chr2:160884600-160885800	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr2:160884600-160885800	Enhancers	Fetal Lung	lung
25	chr2:160884600-160885800	Enhancers	HSMM	muscle
26	chr2:160884800-160886000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:160884800-160886000	Enhancers	Fetal Heart	heart
28	chr2:160885000-160885800	Genic enhancers	HSMMtube	muscle
29	chr2:160885000-160887800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:160885200-160885600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:160885200-160885600	Enhancers	Fetal Brain Male	brain
32	chr2:160885200-160885600	Flanking Active TSS	Ovary	ovary
33	chr2:160885200-160885600	Enhancers	NHLF	lung
34	chr2:160885200-160885600	Flanking Active TSS	Osteobl	bone
35	chr2:160885200-160885800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:160885200-160885800	Enhancers	Right Atrium	heart
37	chr2:160885200-160885800	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr2:160885200-160885800	Enhancers	NH-A	brain
39	chr2:160885200-160886000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:160885200-160886000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr2:160885200-160886000	Strong transcription	Fetal Intestine Large	intestine
42	chr2:160885200-160886000	Strong transcription	Fetal Intestine Small	intestine
43	chr2:160885200-160886000	Enhancers	Left Ventricle	heart
44	chr2:160885200-160886000	Enhancers	Lung	lung
45	chr2:160885200-160886000	Enhancers	Pancreas	Pancrea
46	chr2:160885200-160886000	Enhancers	Right Ventricle	heart
47	chr2:160885200-160886000	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr2:160885400-160885600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr2:160885400-160885800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:160885400-160886000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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