Variant report

Variant	rs9862337
Chromosome Location	chr3:157840492-157840493
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:157826605..157829792-chr3:157838040..157843107,6	K562	blood:
2	chr3:157839952..157841696-chr3:157860084..157861712,2	K562	blood:
3	chr3:157840416..157842184-chr3:157852166..157854407,2	MCF-7	breast:
4	chr3:157836454..157837989-chr3:157840263..157841984,2	K562	blood:
5	chr3:157835764..157837989-chr3:157840263..157842524,2	K562	blood:

Variant related genes	Relation type
ENSG00000174891	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12485440	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12486461	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12696067	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13061378	0.85[EUR][1000 genomes]
rs1581408	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1608100	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1608101	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1609525	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1609526	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1610266	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1610267	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1610268	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4261830	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4317053	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4346508	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4414801	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4431056	0.84[EUR][1000 genomes]
rs4602343	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4622858	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4642075	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4680411	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4680412	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4680413	0.81[ASN][1000 genomes]
rs57665991	0.81[ASN][1000 genomes]
rs6441174	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6770442	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6773505	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6783175	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6789448	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6790608	0.85[EUR][1000 genomes]
rs6794461	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6797626	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6803532	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6803630	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7614572	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7622971	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7624303	0.81[ASN][1000 genomes]
rs7630176	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7647342	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7653039	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9290020	0.86[EUR][1000 genomes]
rs9290021	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9814942	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9820954	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9848433	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9870745	0.82[EUR][1000 genomes]
rs9871021	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9881063	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9883891	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013391	chr3:157505943-158115553	Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv536775	chr3:157505943-158115553	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv829768	chr3:157832878-158012070	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9862337	RP11-538P18.2	cis	Nerve Tibial	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157828600-157845800	Weak transcription	Spleen	Spleen
2	chr3:157828600-157847800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:157828600-157857000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:157828800-157840800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:157828800-157841200	Weak transcription	Left Ventricle	heart
6	chr3:157828800-157847600	Weak transcription	NH-A	brain
7	chr3:157828800-157851000	Weak transcription	Right Ventricle	heart
8	chr3:157829000-157840600	Weak transcription	Fetal Kidney	kidney
9	chr3:157829000-157840800	Weak transcription	Adipose Nuclei	Adipose
10	chr3:157829000-157841000	Weak transcription	Fetal Intestine Large	intestine
11	chr3:157829000-157841200	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:157829000-157841400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:157829000-157849400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:157829200-157840600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:157829200-157840800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:157829200-157841200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr3:157829200-157841200	Weak transcription	Fetal Thymus	thymus
18	chr3:157829200-157841400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:157829200-157841800	Weak transcription	Brain Substantia Nigra	brain
20	chr3:157829200-157842000	Weak transcription	Psoas Muscle	Psoas
21	chr3:157829200-157845400	Weak transcription	HMEC	breast
22	chr3:157829200-157861400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:157829400-157840600	Weak transcription	Fetal Lung	lung
24	chr3:157829600-157840600	Weak transcription	Brain Anterior Caudate	brain
25	chr3:157829600-157840800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:157829600-157841400	Weak transcription	Primary B cells from cord blood	blood
27	chr3:157829800-157840800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr3:157830000-157840600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr3:157830000-157840600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:157830000-157840600	Weak transcription	Thymus	Thymus
31	chr3:157830000-157840800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr3:157830000-157841000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr3:157830000-157841200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:157830000-157841200	Weak transcription	Hela-S3	cervix
35	chr3:157830000-157841400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:157830000-157841400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr3:157830000-157843400	Weak transcription	Small Intestine	intestine
38	chr3:157830000-157866400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:157830200-157840600	Weak transcription	Primary T cells from cord blood	blood
40	chr3:157830200-157840800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr3:157830200-157841400	Weak transcription	HepG2	liver
42	chr3:157830200-157841600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr3:157830400-157845000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:157830600-157841200	Weak transcription	A549	lung
45	chr3:157831400-157840600	Weak transcription	Ovary	ovary
46	chr3:157831800-157841000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr3:157831800-157845800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:157833200-157856200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:157833400-157840800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:157834800-157840800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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