Variant report

Variant	rs1876834
Chromosome Location	chr4:48343693-48343694
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	chr4:48270141..48273598-chr4:48341900..48344865,7	K562	blood:
3	chr4:48341515..48344236-chr4:48506268..48509029,2	K562	blood:
4	chr4:48343572..48346544-chr4:48354204..48356298,2	K562	blood:
5	chr4:48270358..48273390-chr4:48340605..48344777,4	MCF-7	breast:
6	chr4:48269261..48273807-chr4:48342628..48344865,6	K562	blood:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction
ENSG00000135605	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10000288	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10001054	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10003458	0.83[AMR][1000 genomes]
rs10004425	0.84[ASN][1000 genomes]
rs1055720	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1055721	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10938530	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11731199	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13122065	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13141335	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17655838	0.83[AMR][1000 genomes]
rs28464394	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28636546	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs28659782	0.81[ASN][1000 genomes]
rs28690347	0.88[AMR][1000 genomes]
rs4695376	0.82[AMR][1000 genomes]
rs6447631	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6447632	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs66894522	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs68142816	0.80[AMR][1000 genomes]
rs6841390	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6843652	0.81[ASN][1000 genomes]
rs6853315	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7655066	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7658851	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7662325	0.83[AMR][1000 genomes]
rs7688310	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9884339	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9992736	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9995939	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9999482	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1876834	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 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	chr4:48342200-48344200	Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr4:48342200-48344400	Active TSS	Colonic Mucosa	Colon
6	chr4:48342200-48344600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr4:48342200-48345200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr4:48342200-48345200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:48342200-48345200	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr4:48342200-48345200	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr4:48342200-48345400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:48342200-48345400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:48342200-48345400	Active TSS	Brain Anterior Caudate	brain
14	chr4:48342200-48345600	Active TSS	H1 Cell Line	embryonic stem cell
15	chr4:48342200-48345800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:48342400-48344400	Active TSS	Brain Cingulate Gyrus	brain
17	chr4:48342400-48344400	Active TSS	Brain Substantia Nigra	brain
18	chr4:48342400-48344800	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr4:48342400-48344800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:48342400-48344800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr4:48342400-48344800	Active TSS	Brain Hippocampus Middle	brain
22	chr4:48342400-48344800	Active TSS	Esophagus	oesophagus
23	chr4:48342400-48345000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr4:48342400-48345000	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr4:48342400-48345000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:48342400-48345000	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr4:48342400-48345200	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr4:48342400-48345200	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr4:48342400-48345200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:48342400-48345200	Active TSS	Brain Angular Gyrus	brain
31	chr4:48342400-48345200	Active TSS	Colon Smooth Muscle	Colon
32	chr4:48342400-48345200	Active TSS	Fetal Muscle Trunk	muscle
33	chr4:48342400-48345200	Active TSS	Left Ventricle	heart
34	chr4:48342400-48345400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr4:48342400-48345400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr4:48342400-48345400	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr4:48342400-48345400	Active TSS	Ovary	ovary
38	chr4:48342400-48345600	Active TSS	Brain Germinal Matrix	brain
39	chr4:48342400-48346000	Active TSS	Aorta	Aorta
40	chr4:48342400-48346200	Active TSS	Psoas Muscle	Psoas
41	chr4:48342400-48346200	Active TSS	Stomach Smooth Muscle	stomach
42	chr4:48342400-48346600	Active TSS	Right Ventricle	heart
43	chr4:48342600-48343800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr4:48342600-48343800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:48342600-48343800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:48342600-48343800	Active TSS	HepG2	liver
47	chr4:48342600-48344200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr4:48342600-48344200	Active TSS	Adipose Nuclei	Adipose
49	chr4:48342600-48344400	Active TSS	Liver	Liver
50	chr4:48342600-48344400	Active TSS	Fetal Adrenal Gland	Adrenal Gland

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