Variant report

Variant	rs28636546
Chromosome Location	chr4:48376851-48376852
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr4:48376843-48376956	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:48375599..48377309-chr4:48383332..48385949,2	K562	blood:
2	chr4:48367572..48370097-chr4:48374243..48377134,2	K562	blood:
3	chr4:48342254..48344251-chr4:48376571..48378779,2	MCF-7	breast:

Variant related genes	Relation type
SLAIN2	TF binding region
ENSG00000109171	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10000288	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10001054	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10003458	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10004425	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10024547	0.85[ASN][1000 genomes]
rs1055720	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1055721	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10938530	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11731199	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11737752	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13122065	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13141335	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17609600	0.84[ASN][1000 genomes]
rs17655838	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1876834	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs28411210	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28464394	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28659782	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28690347	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4695376	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6447631	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6447632	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66894522	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68142816	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6841390	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6843652	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6853315	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7655066	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7658851	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7662325	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7688310	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7700141	0.81[AFR][1000 genomes]
rs9884339	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9992736	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9995939	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9999482	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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
rs28636546	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48355000-48380000	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr4:48355000-48412600	Weak transcription	Aorta	Aorta
3	chr4:48355200-48377600	Weak transcription	Fetal Intestine Small	intestine
4	chr4:48355200-48379800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:48355800-48390600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr4:48357200-48384600	Weak transcription	Lung	lung
7	chr4:48359200-48384400	Weak transcription	Fetal Muscle Leg	muscle
8	chr4:48361000-48384600	Weak transcription	Fetal Stomach	stomach
9	chr4:48362600-48378000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:48362600-48378200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:48362600-48384600	Weak transcription	Left Ventricle	heart
12	chr4:48363000-48377600	Weak transcription	Psoas Muscle	Psoas
13	chr4:48363000-48380000	Weak transcription	Fetal Lung	lung
14	chr4:48363000-48384600	Weak transcription	Ovary	ovary
15	chr4:48363400-48405400	Weak transcription	Right Ventricle	heart
16	chr4:48363600-48377600	Weak transcription	Osteobl	bone
17	chr4:48363600-48382600	Weak transcription	Fetal Brain Male	brain
18	chr4:48363600-48382800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr4:48364000-48377400	Weak transcription	NHDF-Ad	bronchial
20	chr4:48364000-48381400	Weak transcription	Fetal Heart	heart
21	chr4:48364200-48377600	Weak transcription	NH-A	brain
22	chr4:48364200-48381800	Weak transcription	Adipose Nuclei	Adipose
23	chr4:48364400-48377000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:48368600-48384600	Weak transcription	Thymus	Thymus
25	chr4:48368800-48384600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr4:48369400-48377600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr4:48369400-48377600	Weak transcription	Colonic Mucosa	Colon
28	chr4:48369600-48377400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr4:48369600-48377400	Weak transcription	HMEC	breast
30	chr4:48369600-48382600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr4:48371400-48395400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr4:48371600-48377400	Weak transcription	HUVEC	blood vessel
33	chr4:48371600-48377600	Weak transcription	NHLF	lung
34	chr4:48371600-48377800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr4:48371600-48379600	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr4:48371800-48377800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr4:48372000-48379600	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr4:48372000-48380600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr4:48372000-48384200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr4:48372200-48377600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr4:48372200-48380800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:48372600-48377800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr4:48372600-48377800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr4:48372600-48380000	Weak transcription	Brain Angular Gyrus	brain
45	chr4:48372600-48387000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr4:48372600-48426800	Weak transcription	Small Intestine	intestine
47	chr4:48372800-48377600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr4:48372800-48377600	Weak transcription	Colon Smooth Muscle	Colon
49	chr4:48372800-48377800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr4:48372800-48379600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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