Variant report

Variant	rs392187
Chromosome Location	chr4:48344930-48344931
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48343471..48345353-chr4:48369021..48370568,2	MCF-7	breast:
2	chr4:48343572..48346544-chr4:48354204..48356298,2	K562	blood:
3	chr4:48344085..48345850-chr4:48830456..48833422,2	K562	blood:
4	chr4:48343973..48346063-chr4:48356828..48359174,2	K562	blood:

Variant related genes	Relation type
ENSG00000109180	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10003230	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10026398	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10029785	0.83[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10938534	0.81[JPT][hapmap]
rs1117010	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11945562	0.86[JPT][hapmap]
rs12507206	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12511991	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12645501	0.81[JPT][hapmap]
rs12645951	0.83[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs12649527	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12649528	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13105385	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13115295	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13133788	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13148849	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13150017	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1352433	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1472967	0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1703973	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291474	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2291475	0.83[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2353312	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28409655	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs368609	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs372825	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3828496	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs403495	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs404348	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs404445	0.83[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs404656	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs411261	0.87[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs421336	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs421833	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs429969	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs432927	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs445892	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs449376	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs450498	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62309425	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6447634	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6811148	0.81[JPT][hapmap]
rs6816010	0.83[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs6816352	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6821277	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6829716	0.86[JPT][hapmap]
rs6836632	0.86[JPT][hapmap]
rs6837335	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6848073	0.83[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs6848395	0.81[EUR][1000 genomes]
rs7438704	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7654770	0.86[JPT][hapmap]
rs7668529	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7672892	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7674269	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7678379	0.86[JPT][hapmap]
rs7697851	0.86[JPT][hapmap]
rs7700018	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs923372	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs923373	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9291323	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs937888	0.81[JPT][hapmap]
rs974014	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs974015	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs974016	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs992423	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv3377721	chr4:48342220-48345068	Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs392187	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL
rs392187	OCIAD2	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48342000-48345400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr4:48342000-48345400	Active TSS	Fetal Intestine Large	intestine
3	chr4:48342000-48345600	Active TSS	Fetal Intestine Small	intestine
4	chr4:48342200-48345200	Active TSS	H9 Cell Line	embryonic stem cell
5	chr4:48342200-48345200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:48342200-48345200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr4:48342200-48345200	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr4:48342200-48345400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:48342200-48345400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:48342200-48345400	Active TSS	Brain Anterior Caudate	brain
11	chr4:48342200-48345600	Active TSS	H1 Cell Line	embryonic stem cell
12	chr4:48342200-48345800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:48342400-48345000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr4:48342400-48345000	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr4:48342400-48345000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:48342400-48345000	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr4:48342400-48345200	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr4:48342400-48345200	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr4:48342400-48345200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:48342400-48345200	Active TSS	Brain Angular Gyrus	brain
21	chr4:48342400-48345200	Active TSS	Colon Smooth Muscle	Colon
22	chr4:48342400-48345200	Active TSS	Fetal Muscle Trunk	muscle
23	chr4:48342400-48345200	Active TSS	Left Ventricle	heart
24	chr4:48342400-48345400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:48342400-48345400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr4:48342400-48345400	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr4:48342400-48345400	Active TSS	Ovary	ovary
28	chr4:48342400-48345600	Active TSS	Brain Germinal Matrix	brain
29	chr4:48342400-48346000	Active TSS	Aorta	Aorta
30	chr4:48342400-48346200	Active TSS	Psoas Muscle	Psoas
31	chr4:48342400-48346200	Active TSS	Stomach Smooth Muscle	stomach
32	chr4:48342400-48346600	Active TSS	Right Ventricle	heart
33	chr4:48342600-48345000	Active TSS	Fetal Lung	lung
34	chr4:48342600-48345000	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr4:48342600-48345000	Active TSS	Small Intestine	intestine
36	chr4:48342600-48345000	Active TSS	Osteobl	bone
37	chr4:48342600-48345200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:48342600-48345200	Active TSS	Fetal Brain Female	brain
39	chr4:48342600-48345200	Active TSS	Fetal Kidney	kidney
40	chr4:48342600-48345200	Active TSS	Fetal Thymus	thymus
41	chr4:48342600-48345400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:48342600-48345400	Active TSS	Placenta	Placenta
43	chr4:48342600-48345400	Active TSS	Fetal Stomach	stomach
44	chr4:48342600-48345400	Active TSS	Thymus	Thymus
45	chr4:48342600-48345400	Active TSS	NHDF-Ad	bronchial
46	chr4:48342600-48345600	Active TSS	Fetal Muscle Leg	muscle
47	chr4:48342600-48345600	Active TSS	K562	blood
48	chr4:48342600-48345800	Active TSS	NHLF	lung
49	chr4:48342800-48345000	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr4:48342800-48345000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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