Variant report

Variant	rs774003
Chromosome Location	chr3:138175363-138175364
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10935284	0.90[ASN][1000 genomes]
rs13101081	0.90[ASN][1000 genomes]
rs1379257	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1479930	0.90[ASN][1000 genomes]
rs1600511	0.90[ASN][1000 genomes]
rs1673607	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1679167	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1679168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1679175	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1720836	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2347469	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2607795	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2881793	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4678264	0.90[ASN][1000 genomes]
rs4678265	0.90[ASN][1000 genomes]
rs4678420	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs550507	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs559313	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs586946	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs611134	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs629884	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs680070	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7625326	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7634745	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7643973	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7653815	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs773444	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs774004	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs774005	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs774006	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs774007	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs774008	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs808925	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs811792	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs811793	0.90[ASN][1000 genomes]
rs9811052	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9817419	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9827256	0.84[ASN][1000 genomes]
rs9848718	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9853998	0.90[ASN][1000 genomes]
rs9878436	1.00[JPT][hapmap]
rs9879213	0.82[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs774003	FAIM	Cis_1M	lymphoblastoid	RTeQTL
rs774003	CEP70	Cis_1M	lymphoblastoid	RTeQTL

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	chr3:138156000-138175800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:138161600-138198400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr3:138162400-138177200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:138162800-138178800	Weak transcription	Fetal Intestine Small	intestine
6	chr3:138166600-138183200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:138170800-138198400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:138171000-138193000	Weak transcription	Pancreas	Pancrea
9	chr3:138171200-138185400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:138171400-138198400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:138171600-138175400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:138172400-138176600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:138172400-138181800	Weak transcription	Placenta	Placenta
14	chr3:138172800-138175800	Weak transcription	Fetal Stomach	stomach
15	chr3:138173800-138175400	Strong transcription	Brain Angular Gyrus	brain
16	chr3:138173800-138179000	Strong transcription	Lung	lung
17	chr3:138173800-138181200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:138174200-138180800	Enhancers	Fetal Muscle Trunk	muscle
19	chr3:138174400-138176400	Enhancers	Fetal Muscle Leg	muscle
20	chr3:138174600-138175600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:138174600-138176400	Genic enhancers	Stomach Smooth Muscle	stomach
22	chr3:138174600-138176800	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr3:138174600-138183600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:138174800-138175400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr3:138174800-138175600	Enhancers	Colon Smooth Muscle	Colon
26	chr3:138174800-138177800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:138175000-138175400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:138175000-138175400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:138175000-138175400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:138175000-138175400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:138175000-138175400	Enhancers	Muscle Satellite Cultured Cells	--
32	chr3:138175000-138176000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
33	chr3:138175000-138176800	Enhancers	HSMMtube	muscle
34	chr3:138175200-138175400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:138175200-138175600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:138175200-138176600	Weak transcription	NHEK	skin
37	chr3:138175200-138176800	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr3:138175200-138178600	Weak transcription	Fetal Intestine Large	intestine
39	chr3:138175200-138180400	Weak transcription	Osteobl	bone
40	chr3:138175200-138196000	Weak transcription	Brain Anterior Caudate	brain

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