Variant report

Variant	rs2353312
Chromosome Location	chr4:48369395-48369396
allele	A/G
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	FOS	chr4:48369344-48369395	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:48343471..48345353-chr4:48369021..48370568,2	MCF-7	breast:
2	chr4:48342580..48345517-chr4:48368685..48371694,3	K562	blood:
3	chr4:48367572..48370097-chr4:48374243..48377134,2	K562	blood:
4	chr4:48342718..48345517-chr4:48368685..48371469,2	K562	blood:

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

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10003230	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10026398	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10029785	0.83[ASN][1000 genomes]
rs1117010	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12503644	0.87[ASN][1000 genomes]
rs12507206	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12511991	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12645951	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12649527	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12649528	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13105385	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13115295	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13133788	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13148849	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13150017	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1352433	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1472967	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1586540	0.80[ASN][1000 genomes]
rs1703973	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1948167	0.80[ASN][1000 genomes]
rs2029348	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291474	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291475	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2353315	0.85[ASN][1000 genomes]
rs28409655	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34975258	0.85[ASN][1000 genomes]
rs35758434	0.80[ASN][1000 genomes]
rs368609	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs372825	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3828496	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs392187	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs403495	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs404348	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs404445	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs404656	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs411261	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs421336	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs421833	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs429969	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs432927	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs445892	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs449376	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs450498	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4694895	0.80[ASN][1000 genomes]
rs62309425	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6447634	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6447635	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6816010	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6816352	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6821277	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829705	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6836010	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6837335	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6844211	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6848073	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6848395	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7438704	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7668529	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7672892	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7674269	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7678164	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7700018	0.82[ASN][1000 genomes]
rs923372	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs923373	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9291323	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs974014	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs974015	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs974016	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9996532	0.85[EUR][1000 genomes];0.86[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
rs2353312	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48346600-48371000	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr4:48348800-48371000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr4:48350000-48375800	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr4:48352800-48372400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:48353000-48371200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr4:48355000-48376600	Weak transcription	Primary B cells from cord blood	blood
7	chr4:48355000-48380000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr4:48355000-48412600	Weak transcription	Aorta	Aorta
9	chr4:48355200-48377600	Weak transcription	Fetal Intestine Small	intestine
10	chr4:48355200-48379800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:48355400-48371200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:48355800-48390600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr4:48357200-48384600	Weak transcription	Lung	lung
14	chr4:48358800-48371800	Weak transcription	Small Intestine	intestine
15	chr4:48359200-48384400	Weak transcription	Fetal Muscle Leg	muscle
16	chr4:48361000-48384600	Weak transcription	Fetal Stomach	stomach
17	chr4:48362600-48378000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr4:48362600-48378200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:48362600-48384600	Weak transcription	Left Ventricle	heart
20	chr4:48363000-48377600	Weak transcription	Psoas Muscle	Psoas
21	chr4:48363000-48380000	Weak transcription	Fetal Lung	lung
22	chr4:48363000-48384600	Weak transcription	Ovary	ovary
23	chr4:48363200-48372600	Weak transcription	Brain Anterior Caudate	brain
24	chr4:48363200-48376600	Weak transcription	A549	lung
25	chr4:48363400-48405400	Weak transcription	Right Ventricle	heart
26	chr4:48363600-48371400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:48363600-48371400	Weak transcription	NHLF	lung
28	chr4:48363600-48377600	Weak transcription	Osteobl	bone
29	chr4:48363600-48382600	Weak transcription	Fetal Brain Male	brain
30	chr4:48363600-48382800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr4:48364000-48377400	Weak transcription	NHDF-Ad	bronchial
32	chr4:48364000-48381400	Weak transcription	Fetal Heart	heart
33	chr4:48364200-48377600	Weak transcription	NH-A	brain
34	chr4:48364200-48381800	Weak transcription	Adipose Nuclei	Adipose
35	chr4:48364400-48377000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:48364600-48371600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:48364600-48372400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:48366000-48371000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr4:48367200-48370000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr4:48367600-48371600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:48367800-48370000	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr4:48367800-48372000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr4:48367800-48372000	Enhancers	Liver	Liver
44	chr4:48367800-48372800	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr4:48368200-48369400	Enhancers	NHEK	skin
46	chr4:48368200-48373000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr4:48368400-48370800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr4:48368400-48374400	Weak transcription	Primary T cells from cord blood	blood
49	chr4:48368600-48369400	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr4:48368600-48369400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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