Variant report

Variant	rs61699523
Chromosome Location	chr3:138327951-138327952
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:138310855..138313031-chr3:138326538..138329064,2	K562	blood:
2	chr3:138326713..138328588-chr3:138552751..138555574,2	MCF-7	breast:
3	chr3:138309173..138314814-chr3:138323140..138328328,8	K562	blood:
4	chr19:18391696..18392343-chr3:138327465..138328374,2	Hela-S3	cervix:
5	chr3:138313052..138315422-chr3:138326245..138328582,4	MCF-7	breast:
6	chr3:138327546..138328111-chr5:53813454..53813969,2	Hela-S3	cervix:
7	chr3:138327653..138331722-chr3:138338376..138340210,3	K562	blood:
8	chr3:138311550..138315468-chr3:138324471..138329332,12	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000178996	Chromatin interaction
ENSG00000158234	Chromatin interaction
ENSG00000051382	Chromatin interaction
ENSG00000114107	Chromatin interaction
ENSG00000130522	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10804658	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1082037	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1088055	0.92[AMR][1000 genomes]
rs13101081	0.89[AMR][1000 genomes]
rs1379257	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1479930	0.87[AMR][1000 genomes]
rs1600511	0.87[AMR][1000 genomes]
rs1672928	0.88[EUR][1000 genomes]
rs1672931	0.88[EUR][1000 genomes]
rs1672933	0.87[EUR][1000 genomes]
rs1672936	0.87[EUR][1000 genomes]
rs1672938	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1672939	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1673593	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1673607	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1673612	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1673624	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2348146	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2607795	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2881793	0.94[AMR][1000 genomes]
rs361073	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs361074	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs361075	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs361076	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs361077	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4432674	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4678264	0.84[AMR][1000 genomes]
rs484698	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs550507	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs559313	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs579750	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs586946	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs587005	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs587331	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60513493	0.82[AMR][1000 genomes]
rs609497	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs611134	0.89[AMR][1000 genomes]
rs618792	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs629884	0.93[AMR][1000 genomes]
rs634374	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs642258	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs654528	0.87[EUR][1000 genomes]
rs664928	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6798058	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs680070	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7625326	0.89[AMR][1000 genomes]
rs7627685	0.87[AMR][1000 genomes]
rs7634745	0.81[AMR][1000 genomes]
rs7643973	0.92[AMR][1000 genomes]
rs7653815	0.87[AMR][1000 genomes]
rs773444	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs773445	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs773448	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs773449	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs773452	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs773455	0.88[EUR][1000 genomes]
rs773456	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs811322	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs811793	0.81[AMR][1000 genomes]
rs9811052	0.89[AMR][1000 genomes]
rs9817419	0.92[AMR][1000 genomes]
rs9827256	0.89[AMR][1000 genomes]
rs9848718	0.88[AMR][1000 genomes]
rs9853998	0.88[AMR][1000 genomes]
rs9878436	0.90[AMR][1000 genomes];0.85[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs61699523	FAIM	Cis_1M	lymphoblastoid	RTeQTL
rs61699523	CEP70	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138327000-138328200	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr3:138327000-138328400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:138327000-138328400	Active TSS	NHLF	lung
4	chr3:138327000-138328600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr3:138327000-138328600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:138327000-138328600	Active TSS	Primary T cells from cord blood	blood
7	chr3:138327000-138328800	Active TSS	HSMM	muscle
8	chr3:138327000-138329000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:138327000-138329000	Active TSS	Rectal Smooth Muscle	rectum
10	chr3:138327200-138328000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:138327200-138328200	Active TSS	HSMMtube	muscle
12	chr3:138327200-138328400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
13	chr3:138327200-138328400	Active TSS	Fetal Lung	lung
14	chr3:138327200-138328400	Active TSS	HepG2	liver
15	chr3:138327200-138328600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:138327200-138328600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:138327200-138328600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr3:138327200-138328600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:138327200-138328600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:138327200-138328600	Active TSS	Brain Angular Gyrus	brain
21	chr3:138327200-138328600	Active TSS	Brain Cingulate Gyrus	brain
22	chr3:138327200-138328600	Active TSS	Fetal Brain Female	brain
23	chr3:138327200-138328600	Active TSS	Left Ventricle	heart
24	chr3:138327200-138328600	Active TSS	K562	blood
25	chr3:138327200-138328800	Active TSS	Right Ventricle	heart
26	chr3:138327200-138329000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr3:138327200-138329000	Active TSS	Aorta	Aorta
28	chr3:138327200-138329000	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr3:138327400-138328200	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr3:138327400-138328200	Active TSS	Colon Smooth Muscle	Colon
31	chr3:138327400-138328200	Transcr. at gene 5' and 3'	Right Atrium	heart
32	chr3:138327400-138328400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr3:138327400-138328400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:138327400-138328400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
35	chr3:138327400-138328400	Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr3:138327400-138328400	Active TSS	Fetal Kidney	kidney
37	chr3:138327400-138328400	Active TSS	Gastric	stomach
38	chr3:138327400-138328400	Active TSS	Small Intestine	intestine
39	chr3:138327400-138328400	Active TSS	Hela-S3	cervix
40	chr3:138327400-138328400	Active TSS	Osteobl	bone
41	chr3:138327400-138328600	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr3:138327400-138328600	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr3:138327400-138328600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
44	chr3:138327400-138328600	Active TSS	Brain Hippocampus Middle	brain
45	chr3:138327400-138328600	Active TSS	Brain Substantia Nigra	brain
46	chr3:138327400-138328600	Active TSS	Ovary	ovary
47	chr3:138327400-138328800	Active TSS	Thymus	Thymus
48	chr3:138327400-138329000	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr3:138327400-138329000	Active TSS	A549	lung
50	chr3:138327600-138328200	Active TSS	Primary B cells from peripheral blood	blood

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