Variant report

Variant	rs1679167
Chromosome Location	chr3:138187568-138187569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TFAP2C	chr3:138187565-138188283	Hela-S3	cervix:	n/a	chr3:138188004-138188019

No.	Distal block	Cell Line	Cell type
1	chr3:138186020..138187574-chr3:138189253..138191029,2	K562	blood:
2	chr3:138185730..138189738-chr3:138190908..138194397,4	MCF-7	breast:
3	chr3:138186886..138189284-chr3:138191772..138193552,2	K562	blood:

Variant related genes	Relation type
ESYT3	TF binding region
ENSG00000158220	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10804658	0.89[CEU][hapmap]
rs1082037	0.86[ASN][1000 genomes]
rs1088055	0.86[ASN][1000 genomes]
rs10935281	0.83[EUR][1000 genomes]
rs10935284	1.00[ASN][1000 genomes]
rs12490633	0.82[CEU][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs12636910	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs13085181	0.90[EUR][1000 genomes]
rs13101081	1.00[ASN][1000 genomes]
rs1379257	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.86[ASN][1000 genomes]
rs1479930	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1600511	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1672927	0.82[CEU][hapmap];0.89[TSI][hapmap]
rs1672928	0.81[CEU][hapmap];0.82[MEX][hapmap]
rs1672932	0.82[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs1673593	0.86[ASN][1000 genomes]
rs1673607	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.83[ASN][1000 genomes]
rs1673608	0.82[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs1673622	0.81[CEU][hapmap]
rs1673624	0.80[ASN][1000 genomes]
rs1679165	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1679168	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1679169	0.83[EUR][1000 genomes]
rs1679175	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1720836	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]
rs2347469	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2607795	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs2881793	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.86[ASN][1000 genomes]
rs361073	0.89[CEU][hapmap];0.90[MEX][hapmap]
rs361074	0.89[CEU][hapmap];0.90[MEX][hapmap]
rs361075	0.89[CEU][hapmap];0.90[MEX][hapmap]
rs361076	0.89[CEU][hapmap]
rs361077	0.89[CEU][hapmap];0.90[MEX][hapmap]
rs3884240	0.82[CEU][hapmap];0.89[TSI][hapmap]
rs3884241	0.82[CEU][hapmap]
rs4432674	0.86[ASN][1000 genomes]
rs4678264	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4678265	1.00[ASN][1000 genomes]
rs4678419	0.85[EUR][1000 genomes]
rs4678420	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs484698	0.89[CEU][hapmap];0.90[MEX][hapmap]
rs497334	0.82[CEU][hapmap]
rs503922	0.82[CEU][hapmap];0.89[TSI][hapmap]
rs529615	0.82[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs542010	0.89[TSI][hapmap]
rs550507	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs559160	0.80[MEX][hapmap]
rs559313	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs56236670	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs564800	0.86[TSI][hapmap]
rs586946	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs60513493	0.86[ASN][1000 genomes]
rs609797	0.82[CEU][hapmap];0.87[TSI][hapmap]
rs611134	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.86[ASN][1000 genomes]
rs629884	0.92[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];0.86[ASN][1000 genomes]
rs6439809	0.82[CEU][hapmap]
rs6439810	0.82[CEU][hapmap];0.89[TSI][hapmap]
rs66644444	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67037472	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6763380	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6798058	0.80[ASN][1000 genomes]
rs680070	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7625326	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7626226	0.88[CEU][hapmap]
rs7627685	0.92[CEU][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7634745	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643973	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.86[ASN][1000 genomes]
rs7645920	0.82[CEU][hapmap]
rs7653815	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773444	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs773445	0.86[ASN][1000 genomes]
rs773450	0.82[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs774003	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[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	0.89[CEU][hapmap]
rs808925	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs811322	0.89[CEU][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs811792	0.97[ASN][1000 genomes]
rs811793	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814022	0.82[CEU][hapmap];0.87[TSI][hapmap]
rs936316	0.82[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs9811052	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];1.00[ASN][1000 genomes]
rs9817419	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.86[ASN][1000 genomes]
rs9827256	0.93[ASN][1000 genomes]
rs9848718	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9853998	1.00[ASN][1000 genomes]
rs9878436	0.89[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1679167	FAIM	cis	parietal	SCAN
rs1679167	CEP70	cis	lymphoblastoid	seeQTL
rs1679167	FAIM	cis	cerebellum	SCAN
rs1679167	FAIM	Cis_1M	lymphoblastoid	RTeQTL
rs1679167	FAIM	cis	multi-tissue	Pritchard
rs1679167	CEP70	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138161600-138198400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:138170800-138198400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:138171000-138193000	Weak transcription	Pancreas	Pancrea
4	chr3:138171400-138198400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:138175200-138196000	Weak transcription	Brain Anterior Caudate	brain
6	chr3:138177600-138195400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:138178000-138197000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:138178200-138196000	Weak transcription	Aorta	Aorta
9	chr3:138178800-138188800	Weak transcription	Right Ventricle	heart
10	chr3:138179800-138188600	Weak transcription	Fetal Intestine Small	intestine
11	chr3:138179800-138199400	Weak transcription	Thymus	Thymus
12	chr3:138181000-138187600	Weak transcription	HSMM	muscle
13	chr3:138181200-138192400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:138182800-138187800	Strong transcription	Lung	lung
15	chr3:138183200-138187600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:138184400-138188200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:138184400-138191200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:138184400-138198400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:138185000-138195200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:138185400-138189600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr3:138185600-138187800	Weak transcription	HSMMtube	muscle
22	chr3:138186200-138188200	Strong transcription	Fetal Stomach	stomach
23	chr3:138186200-138190200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:138186400-138187600	Strong transcription	Fetal Muscle Leg	muscle
25	chr3:138186400-138187600	Strong transcription	Stomach Smooth Muscle	stomach
26	chr3:138186400-138187800	Enhancers	Psoas Muscle	Psoas
27	chr3:138186400-138190200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:138186600-138189000	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr3:138186800-138187600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:138187000-138188000	Strong transcription	Brain Cingulate Gyrus	brain
31	chr3:138187000-138190200	Enhancers	Rectal Smooth Muscle	rectum
32	chr3:138187000-138190400	Enhancers	Colon Smooth Muscle	Colon
33	chr3:138187200-138187600	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
34	chr3:138187200-138187600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr3:138187200-138187800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:138187200-138188400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:138187200-138189600	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:138187400-138188200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:138187400-138188200	Enhancers	Left Ventricle	heart
40	chr3:138187400-138188400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:138187400-138188400	Enhancers	Muscle Satellite Cultured Cells	--
42	chr3:138187400-138188400	Enhancers	Hela-S3	cervix
43	chr3:138187400-138188400	Enhancers	NHEK	skin
44	chr3:138187400-138191000	Enhancers	NHDF-Ad	bronchial

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