Variant report

Variant	rs1720836
Chromosome Location	chr3:138180712-138180713
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10804658	0.92[CEU][hapmap]
rs1082037	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1088055	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10935281	0.84[EUR][1000 genomes]
rs10935284	1.00[ASN][1000 genomes]
rs12490633	0.82[MEX][hapmap];0.89[TSI][hapmap]
rs12636910	0.82[CEU][hapmap];0.89[TSI][hapmap]
rs13085181	0.92[EUR][1000 genomes]
rs13101081	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1379257	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1479930	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1600511	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1672927	0.89[TSI][hapmap]
rs1672928	0.85[CEU][hapmap]
rs1672932	0.89[TSI][hapmap]
rs1673593	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1673607	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1673608	0.89[TSI][hapmap]
rs1673624	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1679165	0.87[EUR][1000 genomes]
rs1679167	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679168	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs1679169	0.83[EUR][1000 genomes]
rs1679175	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2347469	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs2348146	0.81[AMR][1000 genomes]
rs2607795	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes]
rs2881793	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs361073	0.92[CEU][hapmap];0.95[MEX][hapmap]
rs361074	0.92[CEU][hapmap];0.95[MEX][hapmap]
rs361075	0.92[CEU][hapmap];0.95[MEX][hapmap]
rs361076	0.92[CEU][hapmap]
rs361077	0.92[CEU][hapmap];0.95[MEX][hapmap]
rs3884240	0.89[TSI][hapmap]
rs4432674	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4678264	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4678265	1.00[ASN][1000 genomes]
rs4678419	0.88[EUR][1000 genomes]
rs4678420	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs484698	0.92[CEU][hapmap];0.95[MEX][hapmap]
rs503922	0.89[TSI][hapmap]
rs529615	0.89[TSI][hapmap]
rs542010	0.89[TSI][hapmap]
rs550507	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs559313	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes]
rs56236670	0.85[EUR][1000 genomes]
rs564800	0.81[MEX][hapmap];0.91[TSI][hapmap]
rs586946	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs587005	0.84[AMR][1000 genomes]
rs587331	0.84[AMR][1000 genomes]
rs60513493	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs609797	0.82[MEX][hapmap];0.91[TSI][hapmap]
rs611134	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs629884	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs634374	0.80[AMR][1000 genomes]
rs6439810	0.89[TSI][hapmap]
rs664928	0.80[AMR][1000 genomes]
rs66644444	0.86[EUR][1000 genomes]
rs67037472	0.89[EUR][1000 genomes]
rs6763380	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs6798058	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs680070	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7625326	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7626226	0.84[CEU][hapmap]
rs7627685	0.89[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7634745	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643973	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7653815	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773444	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs773445	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs773450	0.89[TSI][hapmap]
rs773456	0.80[AMR][1000 genomes]
rs774003	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774004	0.93[ASN][1000 genomes]
rs774005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs774006	0.97[ASN][1000 genomes]
rs774007	0.97[ASN][1000 genomes]
rs774008	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs774015	0.85[CEU][hapmap];0.81[MEX][hapmap]
rs808925	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs811322	0.92[CEU][hapmap];0.90[MEX][hapmap]
rs811792	0.97[ASN][1000 genomes]
rs811793	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814022	0.82[MEX][hapmap];0.91[TSI][hapmap]
rs936316	0.89[TSI][hapmap]
rs9811052	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9817419	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9827256	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9848718	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9853998	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9878436	0.85[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9879213	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv3447663	chr3:138096329-138273034	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv460864	chr3:138100539-138194435	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv591853	chr3:138100539-138194435	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv522517	chr3:138174523-138297982	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1720836	FAIM	cis	Muscle Skeletal	GTEx
rs1720836	FAIM	Cis_1M	lymphoblastoid	RTeQTL
rs1720836	CEP70	cis	Muscle Skeletal	GTEx
rs1720836	FAIM	cis	parietal	SCAN
rs1720836	CEP70	Cis_1M	lymphoblastoid	RTeQTL
rs1720836	FAIM	cis	cerebellum	SCAN
rs1720836	CEP70	cis	lymphoblastoid	seeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138155000-138182800	Weak transcription	Gastric	stomach
2	chr3:138161600-138198400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:138166600-138183200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:138170800-138198400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:138171000-138193000	Weak transcription	Pancreas	Pancrea
6	chr3:138171200-138185400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:138171400-138198400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:138172400-138181800	Weak transcription	Placenta	Placenta
9	chr3:138173800-138181200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:138174200-138180800	Enhancers	Fetal Muscle Trunk	muscle
11	chr3:138174600-138183600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:138175200-138196000	Weak transcription	Brain Anterior Caudate	brain
13	chr3:138176400-138184800	Genic enhancers	Fetal Muscle Leg	muscle
14	chr3:138176800-138187200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:138177200-138181200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:138177600-138187200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:138177600-138195400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:138178000-138197000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:138178200-138196000	Weak transcription	Aorta	Aorta
20	chr3:138178400-138183200	Weak transcription	Colon Smooth Muscle	Colon
21	chr3:138178600-138181200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:138178600-138182600	Weak transcription	Fetal Stomach	stomach
23	chr3:138178600-138187000	Weak transcription	Right Atrium	heart
24	chr3:138178800-138188800	Weak transcription	Right Ventricle	heart
25	chr3:138179000-138181000	Enhancers	HSMM	muscle
26	chr3:138179600-138180800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:138179600-138180800	Enhancers	NHDF-Ad	bronchial
28	chr3:138179600-138181200	Enhancers	HSMMtube	muscle
29	chr3:138179800-138181000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:138179800-138183800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:138179800-138188600	Weak transcription	Fetal Intestine Small	intestine
32	chr3:138179800-138199400	Weak transcription	Thymus	Thymus
33	chr3:138180000-138180800	Enhancers	Muscle Satellite Cultured Cells	--
34	chr3:138180200-138180800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:138180200-138183200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:138180400-138180800	Enhancers	Osteobl	bone
37	chr3:138180400-138181200	ZNF genes & repeats	Lung	lung
38	chr3:138180400-138185600	Weak transcription	Brain Angular Gyrus	brain
39	chr3:138180600-138181000	Weak transcription	Brain Substantia Nigra	brain
40	chr3:138180600-138183200	Weak transcription	Stomach Smooth Muscle	stomach

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