Variant report

Variant	rs28659782
Chromosome Location	chr4:48407544-48407545
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	chr4:48397215..48399762-chr4:48405832..48408129,2	K562	blood:
2	chr4:48396297..48398008-chr4:48407103..48408976,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10000288	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10001054	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10003458	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10004425	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10024547	0.86[ASN][1000 genomes]
rs1055720	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1055721	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10938530	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731199	0.83[ASN][1000 genomes]
rs11737752	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13122065	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13141335	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17609600	0.85[ASN][1000 genomes]
rs17655838	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1876834	0.81[ASN][1000 genomes]
rs28411210	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28464394	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28636546	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28690347	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4695376	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4695382	0.88[AFR][1000 genomes]
rs6447631	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447632	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66894522	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68142816	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6841390	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843652	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6853315	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7655066	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7658851	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7662325	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7688310	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7700141	0.89[AFR][1000 genomes]
rs9884339	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9992736	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9995939	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9999482	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[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	nsv528084	chr4:48387851-48413919	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28659782	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48355000-48412600	Weak transcription	Aorta	Aorta
2	chr4:48372600-48426800	Weak transcription	Small Intestine	intestine
3	chr4:48377800-48423800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:48378000-48423800	Weak transcription	Colon Smooth Muscle	Colon
5	chr4:48382200-48431800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:48383200-48412000	Weak transcription	Fetal Brain Male	brain
7	chr4:48385400-48422000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr4:48387000-48422200	Weak transcription	Colonic Mucosa	Colon
9	chr4:48387400-48424800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:48387600-48431400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr4:48387800-48424600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:48391000-48412600	Weak transcription	Brain Substantia Nigra	brain
13	chr4:48391000-48424800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr4:48391200-48423200	Weak transcription	NHLF	lung
15	chr4:48391200-48424600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr4:48391600-48434000	Weak transcription	Fetal Heart	heart
17	chr4:48395600-48424800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr4:48396200-48422000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr4:48396400-48412400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr4:48397000-48424800	Weak transcription	Stomach Mucosa	stomach
21	chr4:48397400-48424000	Weak transcription	HUVEC	blood vessel
22	chr4:48398800-48423200	Weak transcription	GM12878-XiMat	blood
23	chr4:48399000-48422000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr4:48399000-48423800	Weak transcription	NH-A	brain
25	chr4:48399000-48423800	Weak transcription	NHDF-Ad	bronchial
26	chr4:48399200-48412600	Weak transcription	Brain Hippocampus Middle	brain
27	chr4:48399200-48412600	Weak transcription	HSMMtube	muscle
28	chr4:48399200-48422200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr4:48399200-48426000	Weak transcription	A549	lung
30	chr4:48399400-48412600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr4:48399800-48410800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:48399800-48424400	Weak transcription	Brain Anterior Caudate	brain
33	chr4:48400000-48412600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:48400000-48431000	Weak transcription	Brain Angular Gyrus	brain
35	chr4:48400200-48412600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:48400200-48412600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr4:48400200-48412800	Weak transcription	Fetal Kidney	kidney
38	chr4:48400200-48423200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr4:48400200-48426600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr4:48400400-48407800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr4:48400400-48410000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr4:48400400-48412000	Weak transcription	HSMM	muscle
43	chr4:48404200-48413000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr4:48404600-48412600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr4:48404600-48421800	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr4:48404800-48423600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr4:48405200-48408000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr4:48405200-48412400	Weak transcription	HepG2	liver
49	chr4:48405200-48412800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:48405400-48412000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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