Variant report

Variant	rs454707
Chromosome Location	chr4:48341148-48341149
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48339667..48343042-chr4:48377720..48381453,4	K562	blood:
2	chr4:48270358..48273390-chr4:48340605..48344777,4	MCF-7	breast:
3	chr4:48321470..48323955-chr4:48341055..48342680,2	K562	blood:
4	chr4:48338781..48341525-chr4:48341841..48345420,5	MCF-7	breast:
5	chr4:48270541..48273741-chr4:48337743..48341343,4	K562	blood:

Variant related genes	Relation type
ENSG00000109171	Chromatin interaction
ENSG00000135605	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11732338	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13110483	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13133024	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1472972	0.81[JPT][hapmap]
rs192832	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs309867	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs309869	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs309874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs309876	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs309884	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4599384	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62309397	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[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
rs454707	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48330000-48342400	Weak transcription	Esophagus	oesophagus
2	chr4:48333000-48341800	Weak transcription	A549	lung
3	chr4:48333000-48342400	Weak transcription	Left Ventricle	heart
4	chr4:48334000-48341400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:48334200-48342000	Weak transcription	Fetal Heart	heart
6	chr4:48334200-48342000	Weak transcription	HSMM	muscle
7	chr4:48334200-48342200	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr4:48334200-48342600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:48334400-48342400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:48334800-48341600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:48335800-48342000	Weak transcription	Fetal Kidney	kidney
12	chr4:48336400-48342000	Weak transcription	Osteobl	bone
13	chr4:48337400-48341600	Weak transcription	HSMMtube	muscle
14	chr4:48337600-48341400	Enhancers	K562	blood
15	chr4:48337600-48341800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr4:48337600-48342400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr4:48338400-48341600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:48338400-48341600	Weak transcription	Hela-S3	cervix
19	chr4:48338400-48342200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:48338400-48342200	Weak transcription	Fetal Muscle Leg	muscle
21	chr4:48339000-48341200	Enhancers	Fetal Thymus	thymus
22	chr4:48339000-48341200	Weak transcription	NHDF-Ad	bronchial
23	chr4:48339000-48342000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:48339000-48342200	Enhancers	HMEC	breast
25	chr4:48339200-48341200	Enhancers	Thymus	Thymus
26	chr4:48339200-48341600	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr4:48339400-48342000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr4:48339400-48342200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:48339400-48342400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr4:48339600-48342000	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr4:48339800-48341600	Enhancers	Fetal Lung	lung
32	chr4:48339800-48342200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:48340000-48341400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr4:48340200-48341600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:48340200-48341600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:48340200-48342200	Weak transcription	GM12878-XiMat	blood
37	chr4:48340200-48342200	Enhancers	NHEK	skin
38	chr4:48340400-48342000	Enhancers	Fetal Intestine Small	intestine
39	chr4:48340400-48342000	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr4:48340400-48342200	Enhancers	HepG2	liver
41	chr4:48340400-48342400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr4:48340600-48341600	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr4:48340600-48341600	Weak transcription	Stomach Mucosa	stomach
44	chr4:48340600-48341800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:48340600-48342000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:48340600-48342200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr4:48340600-48342200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr4:48340800-48341800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr4:48340800-48341800	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr4:48340800-48342000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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