Variant report

Variant	rs10004425
Chromosome Location	chr4:48368959-48368960
allele	C/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	chr4:48368722-48369023	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr4:48368795-48369263	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:48342580..48345517-chr4:48368685..48371694,3	K562	blood:
2	chr4:48367572..48370097-chr4:48374243..48377134,2	K562	blood:
3	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: 39 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10000288	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10001054	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10003458	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10024547	0.83[ASN][1000 genomes]
rs10517217	0.82[ASN][1000 genomes]
rs1055720	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1055721	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10938530	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11731199	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11737752	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13122065	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13141335	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17609600	0.82[ASN][1000 genomes]
rs17655838	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1876834	0.84[ASN][1000 genomes]
rs28411210	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28464394	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28636546	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28659782	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28690347	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4695376	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6447631	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6447632	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66894522	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68142816	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6841390	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6843652	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6853315	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7655066	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7658851	0.99[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662325	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7688310	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7700141	0.81[AFR][1000 genomes]
rs9884339	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9992736	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9995939	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9999482	0.99[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[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
rs10004425	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 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	chr4:48353800-48369200	Weak transcription	Pancreas	Pancrea
7	chr4:48355000-48376600	Weak transcription	Primary B cells from cord blood	blood
8	chr4:48355000-48380000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:48355000-48412600	Weak transcription	Aorta	Aorta
10	chr4:48355200-48377600	Weak transcription	Fetal Intestine Small	intestine
11	chr4:48355200-48379800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:48355400-48371200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr4:48355800-48390600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr4:48357200-48384600	Weak transcription	Lung	lung
15	chr4:48358800-48371800	Weak transcription	Small Intestine	intestine
16	chr4:48359200-48384400	Weak transcription	Fetal Muscle Leg	muscle
17	chr4:48361000-48384600	Weak transcription	Fetal Stomach	stomach
18	chr4:48362600-48378000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr4:48362600-48378200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr4:48362600-48384600	Weak transcription	Left Ventricle	heart
21	chr4:48363000-48377600	Weak transcription	Psoas Muscle	Psoas
22	chr4:48363000-48380000	Weak transcription	Fetal Lung	lung
23	chr4:48363000-48384600	Weak transcription	Ovary	ovary
24	chr4:48363200-48372600	Weak transcription	Brain Anterior Caudate	brain
25	chr4:48363200-48376600	Weak transcription	A549	lung
26	chr4:48363400-48405400	Weak transcription	Right Ventricle	heart
27	chr4:48363600-48371400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:48363600-48371400	Weak transcription	NHLF	lung
29	chr4:48363600-48377600	Weak transcription	Osteobl	bone
30	chr4:48363600-48382600	Weak transcription	Fetal Brain Male	brain
31	chr4:48363600-48382800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr4:48363800-48369200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr4:48363800-48369200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr4:48364000-48377400	Weak transcription	NHDF-Ad	bronchial
35	chr4:48364000-48381400	Weak transcription	Fetal Heart	heart
36	chr4:48364200-48369000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr4:48364200-48377600	Weak transcription	NH-A	brain
38	chr4:48364200-48381800	Weak transcription	Adipose Nuclei	Adipose
39	chr4:48364400-48369000	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr4:48364400-48377000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:48364600-48371600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:48364600-48372400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr4:48366000-48371000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr4:48367200-48370000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr4:48367600-48371600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:48367800-48370000	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr4:48367800-48372000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr4:48367800-48372000	Enhancers	Liver	Liver
49	chr4:48367800-48372800	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr4:48368000-48369000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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