Variant report

Variant	rs309869
Chromosome Location	chr4:48339448-48339449
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48338781..48341525-chr4:48341841..48345420,5	MCF-7	breast:
2	chr4:48270541..48273741-chr4:48337743..48341343,4	K562	blood:

Variant related genes	Relation type
ENSG00000135605	Chromatin interaction
ENSG00000109171	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11732338	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13110483	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13133024	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs192832	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309867	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs309874	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309876	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs309884	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs454707	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4599384	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62309397	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs309869	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48330000-48342400	Weak transcription	Esophagus	oesophagus
2	chr4:48331600-48339600	Weak transcription	Stomach Mucosa	stomach
3	chr4:48331600-48340800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:48333000-48341800	Weak transcription	A549	lung
5	chr4:48333000-48342400	Weak transcription	Left Ventricle	heart
6	chr4:48334000-48341400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:48334200-48339600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:48334200-48340200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:48334200-48342000	Weak transcription	Fetal Heart	heart
10	chr4:48334200-48342000	Weak transcription	HSMM	muscle
11	chr4:48334200-48342200	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr4:48334200-48342600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:48334400-48342400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:48334800-48341600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:48335600-48339600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:48335800-48342000	Weak transcription	Fetal Kidney	kidney
17	chr4:48336400-48342000	Weak transcription	Osteobl	bone
18	chr4:48337200-48339800	Weak transcription	Fetal Lung	lung
19	chr4:48337400-48341600	Weak transcription	HSMMtube	muscle
20	chr4:48337600-48341400	Enhancers	K562	blood
21	chr4:48337600-48341800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr4:48337600-48342400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr4:48337800-48339800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:48338200-48340600	Weak transcription	Psoas Muscle	Psoas
25	chr4:48338400-48341000	Weak transcription	NHLF	lung
26	chr4:48338400-48341600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:48338400-48341600	Weak transcription	Hela-S3	cervix
28	chr4:48338400-48342200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:48338400-48342200	Weak transcription	Fetal Muscle Leg	muscle
30	chr4:48339000-48339800	Enhancers	Placenta	Placenta
31	chr4:48339000-48341000	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr4:48339000-48341200	Enhancers	Fetal Thymus	thymus
33	chr4:48339000-48341200	Weak transcription	NHDF-Ad	bronchial
34	chr4:48339000-48342000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:48339000-48342200	Enhancers	HMEC	breast
36	chr4:48339200-48339600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr4:48339200-48341200	Enhancers	Thymus	Thymus
38	chr4:48339200-48341600	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr4:48339400-48340200	Flanking Active TSS	NHEK	skin
40	chr4:48339400-48340600	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr4:48339400-48342000	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr4:48339400-48342200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:48339400-48342400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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