Variant report

Variant	rs56236670
Chromosome Location	chr3:138173905-138173906
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:138169355..138171117-chr3:138172389..138174530,2	MCF-7	breast:
2	chr3:138159991..138162907-chr3:138171980..138174435,2	MCF-7	breast:
3	chr3:138173174..138174919-chr3:138181076..138182864,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10935281	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11709290	0.83[ASN][1000 genomes]
rs13085181	0.83[EUR][1000 genomes]
rs1679165	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1679167	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1679169	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1679175	0.86[EUR][1000 genomes]
rs1720836	0.85[EUR][1000 genomes]
rs3813264	0.81[ASN][1000 genomes]
rs4678266	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4678418	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4678419	0.80[EUR][1000 genomes]
rs66644444	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67037472	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6763380	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9848938	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56236670	FAIM	cis	Muscle Skeletal	GTEx
rs56236670	FAIM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 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	chr3:138169800-138174000	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:138170200-138174200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:138170800-138198400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:138171000-138175000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:138171000-138193000	Weak transcription	Pancreas	Pancrea
12	chr3:138171200-138185400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:138171400-138198400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:138171600-138175400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:138171800-138174600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:138171800-138174600	Weak transcription	NHEK	skin
17	chr3:138171800-138175000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:138172400-138174800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:138172400-138176600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:138172400-138181800	Weak transcription	Placenta	Placenta
21	chr3:138172800-138175800	Weak transcription	Fetal Stomach	stomach
22	chr3:138173400-138174000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:138173600-138174000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:138173800-138174000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:138173800-138174600	Strong transcription	Stomach Smooth Muscle	stomach
26	chr3:138173800-138175000	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:138173800-138175400	Strong transcription	Brain Angular Gyrus	brain
28	chr3:138173800-138179000	Strong transcription	Lung	lung
29	chr3:138173800-138181200	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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