Variant report

Variant	rs1679169
Chromosome Location	chr3:138195529-138195530
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138194164..138195969-chr3:138327251..138329519,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158234	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1082034	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10935281	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10935282	0.90[ASN][1000 genomes]
rs10935287	0.82[AMR][1000 genomes]
rs11709290	0.94[ASN][1000 genomes]
rs12487652	0.82[AMR][1000 genomes]
rs12487694	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12490633	1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs12497070	0.82[AMR][1000 genomes]
rs12636910	0.81[AMR][1000 genomes]
rs13098789	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1625751	0.88[ASN][1000 genomes]
rs1672927	0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1672932	1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs1672963	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1673594	0.80[AFR][1000 genomes]
rs1673608	0.81[AMR][1000 genomes]
rs1673622	0.93[YRI][hapmap];0.82[AMR][1000 genomes]
rs1679165	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1679167	0.83[EUR][1000 genomes]
rs1679175	0.82[EUR][1000 genomes]
rs1720833	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1720836	0.83[EUR][1000 genomes]
rs2086351	0.88[ASN][1000 genomes]
rs2607790	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs28719641	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35471402	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3813264	0.96[ASN][1000 genomes]
rs3884240	0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3884241	0.93[YRI][hapmap]
rs4678266	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4678418	0.81[AMR][1000 genomes]
rs4894389	0.80[ASN][1000 genomes]
rs497334	1.00[YRI][hapmap]
rs503922	0.82[AMR][1000 genomes]
rs529615	0.83[AMR][1000 genomes]
rs537210	0.81[EUR][1000 genomes]
rs542010	0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56236670	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs564800	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs582386	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs609797	0.81[EUR][1000 genomes]
rs612471	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs620035	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6439809	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6439810	0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66644444	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67037472	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6762114	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6763380	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6771237	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73229526	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7626226	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7645920	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs773450	0.93[YRI][hapmap];0.81[AMR][1000 genomes]
rs774011	0.88[ASN][1000 genomes]
rs774012	0.88[ASN][1000 genomes]
rs814022	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs936316	0.93[YRI][hapmap];0.81[AMR][1000 genomes]
rs9822037	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9823182	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9848938	0.94[ASN][1000 genomes]
rs9855306	0.88[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1679169	FAIM	Cis_1M	lymphoblastoid	RTeQTL
rs1679169	FAIM	cis	Muscle Skeletal	GTEx

Chromatin state (count:31 , 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	chr3:138171400-138198400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:138175200-138196000	Weak transcription	Brain Anterior Caudate	brain
5	chr3:138178000-138197000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:138178200-138196000	Weak transcription	Aorta	Aorta
7	chr3:138179800-138199400	Weak transcription	Thymus	Thymus
8	chr3:138184400-138198400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:138187600-138197000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:138188000-138210800	Weak transcription	Lung	lung
11	chr3:138188000-138211600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:138188200-138196200	Strong transcription	Fetal Muscle Leg	muscle
13	chr3:138188200-138197400	Weak transcription	HSMM	muscle
14	chr3:138188200-138197600	Weak transcription	HSMMtube	muscle
15	chr3:138188400-138196400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:138189600-138198400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:138189800-138197800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:138190000-138210800	Weak transcription	Psoas Muscle	Psoas
19	chr3:138190800-138196200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:138191200-138195800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr3:138191600-138195600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:138191800-138198600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:138191800-138203800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:138192000-138198400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:138194000-138260200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:138194400-138198400	Weak transcription	Fetal Heart	heart
27	chr3:138195200-138195600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:138195200-138196800	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr3:138195200-138197800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:138195400-138195600	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr3:138195400-138196800	Enhancers	Skeletal Muscle Male	skeletal muscle

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