Variant report

Variant	rs6853315
Chromosome Location	chr4:48362577-48362578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48361503..48363446-chr4:48370042..48372721,2	K562	blood:
2	chr4:48341877..48344426-chr4:48361149..48363028,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109171	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10000288	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10001054	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10003458	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10004425	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10024547	0.80[ASN][1000 genomes]
rs10517217	0.85[ASN][1000 genomes]
rs1055720	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1055721	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10938530	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11731199	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11737752	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13122065	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13141335	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17655838	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1876834	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28411210	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28464394	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28636546	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28659782	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28690347	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4695376	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6447631	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6447632	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66894522	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68142816	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6841390	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6843652	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7655066	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7658851	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7662325	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7688310	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9884339	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9992736	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9995939	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9999482	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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
rs6853315	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48346000-48362800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr4:48346600-48371000	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr4:48347600-48365000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:48348800-48363000	Weak transcription	Hela-S3	cervix
5	chr4:48348800-48371000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr4:48349600-48363200	Weak transcription	Adipose Nuclei	Adipose
7	chr4:48349600-48364400	Weak transcription	Right Atrium	heart
8	chr4:48350000-48375800	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr4:48351400-48362600	Weak transcription	A549	lung
10	chr4:48352800-48372400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr4:48353000-48371200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr4:48353200-48362800	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:48353200-48362800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr4:48353600-48363200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:48353800-48369200	Weak transcription	Pancreas	Pancrea
16	chr4:48355000-48376600	Weak transcription	Primary B cells from cord blood	blood
17	chr4:48355000-48380000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr4:48355000-48412600	Weak transcription	Aorta	Aorta
19	chr4:48355200-48363200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:48355200-48377600	Weak transcription	Fetal Intestine Small	intestine
21	chr4:48355200-48379800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:48355400-48363000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr4:48355400-48371200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:48355800-48390600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr4:48356000-48362800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr4:48356600-48367800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr4:48357200-48384600	Weak transcription	Lung	lung
28	chr4:48358400-48367000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr4:48358600-48363200	Weak transcription	Liver	Liver
30	chr4:48358800-48362800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr4:48358800-48371800	Weak transcription	Small Intestine	intestine
32	chr4:48359200-48384400	Weak transcription	Fetal Muscle Leg	muscle
33	chr4:48359600-48362600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:48361000-48384600	Weak transcription	Fetal Stomach	stomach
35	chr4:48361600-48363000	Enhancers	Osteobl	bone
36	chr4:48361600-48363600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:48361800-48364000	Enhancers	HMEC	breast
38	chr4:48362000-48363400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr4:48362200-48362600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:48362200-48362600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:48362200-48362600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr4:48362200-48362600	Enhancers	Placenta	Placenta
43	chr4:48362200-48362600	Enhancers	Left Ventricle	heart
44	chr4:48362200-48362800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:48362200-48362800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:48362200-48362800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr4:48362200-48363000	Enhancers	Brain Substantia Nigra	brain
48	chr4:48362200-48363200	Enhancers	Brain Anterior Caudate	brain
49	chr4:48362200-48363400	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr4:48362200-48363400	Enhancers	Skeletal Muscle Male	skeletal muscle

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