Variant report

Variant	rs1479930
Chromosome Location	chr3:138209344-138209345
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10804658	0.89[CEU][hapmap];0.87[AMR][1000 genomes]
rs1082037	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1088055	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10935284	1.00[ASN][1000 genomes]
rs12490633	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs12636910	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs13098789	0.81[EUR][1000 genomes]
rs13101081	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1379257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1600511	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1630766	0.84[AFR][1000 genomes]
rs1672927	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs1672928	0.81[CEU][hapmap]
rs1672932	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs1672938	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1672939	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1673593	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1673607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1673608	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs1673612	0.87[AMR][1000 genomes]
rs1673622	0.88[CEU][hapmap]
rs1673624	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1679167	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679168	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1679175	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1720836	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2347469	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2348146	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2607795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2881793	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35471402	0.83[EUR][1000 genomes]
rs361073	0.89[CEU][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes]
rs361074	0.89[CEU][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes]
rs361075	0.89[CEU][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes]
rs361076	0.89[CEU][hapmap];0.87[AMR][1000 genomes]
rs361077	0.89[CEU][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes]
rs3884240	0.89[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs3884241	0.89[CEU][hapmap]
rs4432674	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4678264	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4678265	1.00[ASN][1000 genomes]
rs4678266	0.88[EUR][1000 genomes]
rs4678420	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs484698	0.88[ASW][hapmap];0.89[CEU][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes]
rs497334	0.89[CEU][hapmap]
rs503922	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs529615	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs542010	0.85[CEU][hapmap];0.91[TSI][hapmap]
rs550507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs559313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs564800	0.85[CEU][hapmap];0.93[TSI][hapmap]
rs579750	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs586946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs587005	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs587331	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60513493	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs609497	0.87[AMR][1000 genomes]
rs609797	0.89[CEU][hapmap];0.93[TSI][hapmap]
rs611134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61699523	0.87[AMR][1000 genomes]
rs618792	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs629884	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs634374	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs642258	0.81[AMR][1000 genomes]
rs6439809	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs6439810	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs664928	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6762114	0.83[EUR][1000 genomes]
rs6798058	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs680070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73229526	0.81[EUR][1000 genomes]
rs7625326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626226	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs7627685	1.00[CEU][hapmap];0.94[GIH][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7634745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7645920	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs7653815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs773445	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs773448	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs773449	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs773450	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs773452	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs773456	0.88[AMR][1000 genomes]
rs774003	1.00[CHB][hapmap];1.00[JPT][hapmap];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	0.82[CEU][hapmap]
rs808925	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs811322	0.89[CEU][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs811792	0.97[ASN][1000 genomes]
rs811793	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814022	0.89[CEU][hapmap];0.93[TSI][hapmap]
rs936316	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs9811052	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9817419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9822037	0.83[EUR][1000 genomes]
rs9827256	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9848718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853998	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878436	0.89[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9879213	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
5	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1479930	FAIM	cis	parietal	SCAN
rs1479930	CEP70	cis	lymphoblastoid	seeQTL
rs1479930	FAIM	cis	cerebellum	SCAN
rs1479930	ESYT3	cis	cerebellum	SCAN
rs1479930	FAIM	cis	multi-tissue	Pritchard

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138188000-138210800	Weak transcription	Lung	lung
2	chr3:138188000-138211600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:138190000-138210800	Weak transcription	Psoas Muscle	Psoas
4	chr3:138194000-138260200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:138199400-138211600	Weak transcription	Fetal Heart	heart
6	chr3:138204800-138211000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:138205000-138211600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:138206800-138210800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:138207000-138210800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:138207000-138223800	Weak transcription	Brain Anterior Caudate	brain
11	chr3:138207600-138211800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:138208200-138210800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:138208200-138211000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr3:138208200-138211400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:138208400-138210800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr3:138208400-138211800	Weak transcription	Fetal Muscle Leg	muscle
17	chr3:138208400-138212200	Weak transcription	HSMM	muscle
18	chr3:138208400-138227400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:138208600-138211200	Weak transcription	Fetal Thymus	thymus
20	chr3:138208600-138215000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:138208800-138211200	Weak transcription	Liver	Liver
22	chr3:138208800-138211200	Weak transcription	Fetal Intestine Small	intestine
23	chr3:138208800-138213400	Weak transcription	Colon Smooth Muscle	Colon
24	chr3:138209000-138211000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:138209000-138211600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:138209200-138218400	Weak transcription	Gastric	stomach

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