Variant report

Variant	rs340165
Chromosome Location	chr3:111832120-111832121
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10934145	0.88[CEU][hapmap]
rs11707558	0.88[CEU][hapmap]
rs11824	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11922559	0.88[CEU][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap]
rs12488760	0.88[CEU][hapmap]
rs12634769	0.88[CEU][hapmap]
rs13066495	0.85[CEU][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs13074229	0.92[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13081485	0.80[CEU][hapmap]
rs13081935	0.81[CEU][hapmap]
rs13082509	0.81[CEU][hapmap]
rs13087086	0.81[CEU][hapmap]
rs13091454	0.82[CEU][hapmap]
rs13100724	0.81[CEU][hapmap]
rs2120095	0.81[CEU][hapmap]
rs340163	0.89[CEU][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes]
rs340172	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856723	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4234412	0.88[CEU][hapmap]
rs4234413	0.88[CEU][hapmap]
rs4282033	0.88[CEU][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap]
rs4392388	0.88[CEU][hapmap]
rs4401342	0.88[CEU][hapmap]
rs4505669	0.88[CEU][hapmap]
rs4560270	0.87[CEU][hapmap]
rs4572740	0.81[CEU][hapmap]
rs4585166	0.81[CEU][hapmap]
rs4632517	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs4682097	0.87[CEU][hapmap]
rs4682355	0.87[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs4682357	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4682380	0.88[CEU][hapmap]
rs6773916	0.92[CEU][hapmap]
rs6781344	0.88[CEU][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap]
rs6798551	0.88[CEU][hapmap]
rs729641	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs746026	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs746027	0.82[EUR][1000 genomes]
rs7613061	0.88[CEU][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap]
rs7616261	0.88[CEU][hapmap]
rs7624367	0.88[CEU][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap]
rs7638520	0.88[CEU][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap]
rs923745	0.94[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9758396	0.88[CEU][hapmap]
rs9809384	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs9809404	0.88[CEU][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap]
rs9822786	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs9823421	0.88[CEU][hapmap]
rs9826043	0.88[CEU][hapmap]
rs9847574	0.86[CEU][hapmap]
rs9860819	0.88[CEU][hapmap]
rs9863061	0.84[CEU][hapmap]
rs9878213	0.88[CEU][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap]
rs9879184	0.88[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755927	chr3:111794310-111834310	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs340165	GCET2	cis	parietal	SCAN
rs340165	CD200	cis	parietal	SCAN
rs340165	SLC9A10	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111810400-111852000	Weak transcription	Esophagus	oesophagus
2	chr3:111812000-111844000	Weak transcription	Colonic Mucosa	Colon
3	chr3:111812000-111845600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr3:111812200-111853000	Weak transcription	Right Ventricle	heart
5	chr3:111812400-111835800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:111812600-111840200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:111814400-111836000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:111817200-111833600	Weak transcription	HSMMtube	muscle
9	chr3:111819000-111840400	Weak transcription	Fetal Stomach	stomach
10	chr3:111819600-111847800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:111821000-111835800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:111821200-111833800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:111821200-111833800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:111821200-111834000	Weak transcription	HSMM	muscle
15	chr3:111821200-111843600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:111821400-111839000	Weak transcription	Osteobl	bone
17	chr3:111821400-111843600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:111821600-111834800	Weak transcription	HUVEC	blood vessel
19	chr3:111822000-111844600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:111822400-111839200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:111822600-111833600	Weak transcription	Fetal Intestine Small	intestine
22	chr3:111822800-111835600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:111823000-111834400	Weak transcription	A549	lung
24	chr3:111823400-111837800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:111825600-111833600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:111825600-111838600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:111825800-111835400	Weak transcription	Aorta	Aorta
28	chr3:111825800-111835600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:111825800-111844400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:111826000-111833800	Weak transcription	Primary T cells from cord blood	blood
31	chr3:111827000-111838600	Weak transcription	Spleen	Spleen
32	chr3:111828000-111833200	Strong transcription	NH-A	brain
33	chr3:111828200-111838600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:111828400-111833800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:111828400-111838200	Weak transcription	Stomach Mucosa	stomach
36	chr3:111828600-111833600	Weak transcription	Gastric	stomach
37	chr3:111828600-111835600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr3:111828800-111835600	Weak transcription	Left Ventricle	heart
39	chr3:111829200-111833200	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr3:111829600-111836400	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:111830000-111834200	Strong transcription	Pancreas	Pancrea
42	chr3:111830000-111835600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr3:111830000-111837800	Strong transcription	NHEK	skin
44	chr3:111830400-111832200	Enhancers	GM12878-XiMat	blood
45	chr3:111830600-111834000	Enhancers	Fetal Thymus	thymus
46	chr3:111830600-111835600	Enhancers	Thymus	Thymus
47	chr3:111830600-111853200	Weak transcription	Lung	lung
48	chr3:111830800-111833600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:111830800-111834000	Weak transcription	Fetal Heart	heart
50	chr3:111830800-111834600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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