Variant report

Variant	rs811322
Chromosome Location	chr3:138329862-138329863
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:138328930..138332756-chr3:138333514..138336895,4	K562	blood:
2	chr3:138329273..138330839-chr3:138333514..138335193,2	K562	blood:
3	chr3:138328883..138330750-chr3:138369541..138371730,2	MCF-7	breast:
4	chr3:138327653..138331722-chr3:138338376..138340210,3	K562	blood:

Variant related genes	Relation type
ENSG00000158234	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs1068685	1.00[CHB][hapmap]
rs10804658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1082037	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1088055	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1091528	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12490633	0.82[MEX][hapmap];0.83[TSI][hapmap]
rs12636910	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs13101081	0.84[AMR][1000 genomes]
rs1379257	0.89[CEU][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1600511	0.81[AMR][1000 genomes]
rs1663554	1.00[CHB][hapmap]
rs1672927	0.83[TSI][hapmap]
rs1672928	0.92[CEU][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs1672931	0.89[EUR][1000 genomes]
rs1672932	0.83[TSI][hapmap]
rs1672933	0.87[EUR][1000 genomes]
rs1672936	0.87[EUR][1000 genomes]
rs1672938	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1672939	0.81[EUR][1000 genomes]
rs1673593	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1673597	1.00[CHB][hapmap]
rs1673607	0.88[ASW][hapmap];0.89[CEU][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1673608	0.83[TSI][hapmap]
rs1673612	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1673622	0.81[CEU][hapmap]
rs1673624	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1679167	0.89[CEU][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs1720836	0.92[CEU][hapmap];0.90[MEX][hapmap]
rs17282752	1.00[JPT][hapmap]
rs191714	1.00[CHB][hapmap]
rs191775	1.00[CHB][hapmap]
rs2348146	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2607795	0.94[ASW][hapmap];0.89[CEU][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2607796	1.00[CHB][hapmap]
rs2881793	0.89[CEU][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes]
rs361057	1.00[CHB][hapmap]
rs361059	1.00[CHB][hapmap]
rs361060	1.00[CHB][hapmap]
rs361061	1.00[CHB][hapmap]
rs361062	1.00[CHB][hapmap]
rs361063	1.00[CHB][hapmap]
rs361066	1.00[CHB][hapmap]
rs361067	1.00[CHB][hapmap]
rs361071	1.00[CHB][hapmap]
rs361072	1.00[CHB][hapmap]
rs361073	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361074	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361075	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361077	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361080	1.00[CHB][hapmap]
rs361082	1.00[CHB][hapmap]
rs361087	1.00[CHB][hapmap]
rs361088	1.00[CHB][hapmap]
rs361096	1.00[CHB][hapmap]
rs385254	1.00[CHB][hapmap];0.81[MEX][hapmap]
rs3884240	0.83[TSI][hapmap]
rs413147	1.00[CHB][hapmap];0.85[MEX][hapmap]
rs4305444	1.00[CHB][hapmap]
rs4432674	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs484698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493152	1.00[CHB][hapmap]
rs497900	1.00[CHB][hapmap]
rs500687	1.00[CHB][hapmap]
rs503922	0.83[TSI][hapmap]
rs520904	1.00[CHB][hapmap]
rs523975	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs524164	1.00[CHB][hapmap]
rs529615	0.83[TSI][hapmap]
rs531577	1.00[CHB][hapmap]
rs537894	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs542010	0.83[TSI][hapmap]
rs550507	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs558905	1.00[CHB][hapmap];0.81[MEX][hapmap]
rs559160	1.00[CHB][hapmap]
rs559313	0.88[ASW][hapmap];0.89[CEU][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs564455	1.00[CHB][hapmap];0.81[MEX][hapmap]
rs564800	0.81[MEX][hapmap];0.81[TSI][hapmap]
rs579750	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs586946	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs587005	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs587331	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs600590	1.00[CHB][hapmap]
rs601032	1.00[CHB][hapmap]
rs603723	1.00[CHB][hapmap]
rs609497	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs609797	0.82[MEX][hapmap];0.81[TSI][hapmap]
rs611134	0.83[ASW][hapmap];0.89[CEU][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61699523	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs618792	0.83[EUR][1000 genomes]
rs624099	1.00[CHB][hapmap]
rs629884	0.89[CEU][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes]
rs634374	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs635592	1.00[CHB][hapmap]
rs642258	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643620	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6439810	0.83[TSI][hapmap]
rs654528	0.88[EUR][1000 genomes]
rs664928	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6798058	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs680070	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7625326	0.89[CEU][hapmap];0.84[AMR][1000 genomes]
rs7626226	0.84[CEU][hapmap]
rs7627685	0.88[ASW][hapmap];0.89[CEU][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap];0.81[AMR][1000 genomes]
rs7634745	0.89[CEU][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs7643722	1.00[CHB][hapmap]
rs7643973	0.94[ASW][hapmap];0.89[CEU][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7653815	0.88[ASW][hapmap];0.89[CEU][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs773045	1.00[CHB][hapmap]
rs773444	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs773445	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs773448	0.84[EUR][1000 genomes]
rs773449	0.85[EUR][1000 genomes]
rs773450	0.83[TSI][hapmap]
rs773452	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs773455	0.89[EUR][1000 genomes]
rs773456	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774015	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[MEX][hapmap]
rs814022	0.82[MEX][hapmap];0.81[TSI][hapmap]
rs936316	0.83[TSI][hapmap]
rs9811052	0.89[CEU][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs9817419	0.94[ASW][hapmap];0.89[CEU][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9822714	1.00[CHB][hapmap]
rs9827256	0.84[AMR][1000 genomes]
rs9834963	1.00[CHB][hapmap]
rs9848718	0.88[CEU][hapmap];0.82[AMR][1000 genomes]
rs9853998	0.82[AMR][1000 genomes]
rs9878436	0.92[CEU][hapmap];0.81[LWK][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active 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
5	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs811322	FAIM	cis	parietal	SCAN
rs811322	CEP70	Cis_1M	lymphoblastoid	RTeQTL
rs811322	FAIM	cis	cerebellum	SCAN
rs811322	FAIM	Cis_1M	lymphoblastoid	RTeQTL
rs811322	CEP70	cis	lymphoblastoid	seeQTL
rs811322	FAIM	cis	multi-tissue	Pritchard

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138328400-138330400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:138328400-138335200	Weak transcription	Gastric	stomach
3	chr3:138328400-138350200	Weak transcription	Lung	lung
4	chr3:138328400-138353200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:138328400-138355000	Weak transcription	Esophagus	oesophagus
6	chr3:138328600-138330600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:138328600-138330800	Enhancers	Pancreas	Pancrea
8	chr3:138328600-138346400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:138328600-138349400	Weak transcription	Ovary	ovary
10	chr3:138328600-138358000	Weak transcription	Psoas Muscle	Psoas
11	chr3:138328800-138344800	Weak transcription	NHDF-Ad	bronchial
12	chr3:138328800-138358000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:138329000-138330200	Weak transcription	Brain Germinal Matrix	brain
14	chr3:138329000-138330400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:138329000-138330400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:138329000-138330400	Weak transcription	HepG2	liver
17	chr3:138329000-138330800	Enhancers	Fetal Thymus	thymus
18	chr3:138329000-138331400	Enhancers	Dnd41	blood
19	chr3:138329000-138333200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:138329000-138333800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:138329000-138333800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:138329000-138334400	Weak transcription	Adipose Nuclei	Adipose
23	chr3:138329000-138336200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:138329000-138337600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:138329000-138338200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:138329000-138342200	Weak transcription	Fetal Stomach	stomach
27	chr3:138329000-138342800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:138329000-138344800	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:138329000-138346800	Weak transcription	Fetal Muscle Leg	muscle
30	chr3:138329000-138347600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:138329000-138348000	Weak transcription	Fetal Intestine Large	intestine
32	chr3:138329000-138348200	Weak transcription	Left Ventricle	heart
33	chr3:138329000-138348400	Weak transcription	Aorta	Aorta
34	chr3:138329000-138348400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:138329000-138348600	Weak transcription	Fetal Intestine Small	intestine
36	chr3:138329000-138350000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr3:138329000-138354200	Weak transcription	Fetal Lung	lung
38	chr3:138329200-138330200	Weak transcription	Fetal Heart	heart
39	chr3:138329200-138330400	Weak transcription	K562	blood
40	chr3:138329200-138330600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:138329200-138330800	Enhancers	Thymus	Thymus
42	chr3:138329200-138331400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr3:138329200-138331400	Weak transcription	NHEK	skin
44	chr3:138329200-138334200	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr3:138329200-138337600	Weak transcription	Colon Smooth Muscle	Colon
46	chr3:138329200-138342200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:138329200-138344600	Weak transcription	Osteobl	bone
48	chr3:138329200-138345000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr3:138329200-138348200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:138329600-138330000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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