Variant report

Variant	rs619679
Chromosome Location	chr12:121291757-121291758
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:121291111..121293734-chr12:121317316..121319397,2	K562	blood:
2	chr12:121291153..121292656-chr12:121442284..121444744,2	MCF-7	breast:
3	chr12:121284720..121286332-chr12:121290544..121292082,2	K562	blood:
4	chr12:121290673..121292534-chr12:121340844..121343138,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157837	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1067742	0.95[ASN][1000 genomes]
rs1105416	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11065286	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1151850	0.85[ASN][1000 genomes]
rs1151851	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1151852	0.85[ASN][1000 genomes]
rs1151861	0.91[ASN][1000 genomes]
rs1151863	0.91[ASN][1000 genomes]
rs1151864	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1168945	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1168954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1168956	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1696363	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1718211	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1732405	0.91[ASN][1000 genomes]
rs2454729	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2649996	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2649998	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2650006	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2701174	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2701178	0.88[ASN][1000 genomes]
rs4767938	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs482522	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs487310	0.88[CHB][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs487912	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs491602	0.97[ASN][1000 genomes]
rs493811	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs497273	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs520405	0.81[ASN][1000 genomes]
rs532140	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs532703	0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs538785	0.97[ASN][1000 genomes]
rs550349	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs551087	0.90[JPT][hapmap]
rs551125	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs564120	0.81[ASN][1000 genomes]
rs566994	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs584001	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs586305	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs589699	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs594507	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs597203	0.81[ASN][1000 genomes]
rs610578	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs618849	0.95[ASN][1000 genomes]
rs628771	0.97[ASN][1000 genomes]
rs631168	0.97[ASN][1000 genomes]
rs633084	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs634850	0.81[EUR][1000 genomes]
rs6553	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs656933	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs662284	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs662739	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs674021	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs679833	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs680303	0.81[ASN][1000 genomes]
rs683091	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs683437	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs688402	0.89[CHB][hapmap]
rs694303	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs708785	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs791210	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs791707	0.82[ASN][1000 genomes]
rs791713	0.97[ASN][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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv3405224	chr12:121289394-121291942	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs619679	SPPL3	cis	Adipose Subcutaneous	GTEx
rs619679	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121274200-121291800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr12:121274800-121291800	Weak transcription	Dnd41	blood
3	chr12:121281600-121296200	Weak transcription	HepG2	liver
4	chr12:121282000-121308600	Weak transcription	Fetal Kidney	kidney
5	chr12:121283200-121310200	Weak transcription	Placenta	Placenta
6	chr12:121283400-121291800	Weak transcription	Pancreas	Pancrea
7	chr12:121283400-121307400	Weak transcription	Esophagus	oesophagus
8	chr12:121283600-121295600	Weak transcription	Fetal Stomach	stomach
9	chr12:121283600-121302200	Weak transcription	Lung	lung
10	chr12:121284000-121294400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:121284600-121292800	Enhancers	Primary B cells from peripheral blood	blood
12	chr12:121286000-121291800	Weak transcription	Fetal Intestine Small	intestine
13	chr12:121286400-121293800	Weak transcription	Right Ventricle	heart
14	chr12:121286600-121293600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:121287600-121293400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:121287600-121294000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:121287800-121300400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr12:121288000-121292800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr12:121288000-121293400	Weak transcription	Brain Substantia Nigra	brain
20	chr12:121288000-121294400	Weak transcription	Right Atrium	heart
21	chr12:121288000-121294600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr12:121288000-121300200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr12:121288000-121311800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:121288000-121316600	Weak transcription	NHLF	lung
25	chr12:121288200-121293800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:121288200-121339600	Weak transcription	Hela-S3	cervix
27	chr12:121288600-121292800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr12:121288600-121293800	Weak transcription	HSMM	muscle
29	chr12:121289800-121292000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:121289800-121293600	Weak transcription	Brain Anterior Caudate	brain
31	chr12:121289800-121294400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr12:121289800-121294600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr12:121289800-121296000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr12:121289800-121297800	Weak transcription	Ovary	ovary
35	chr12:121290000-121291800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr12:121290000-121293400	Weak transcription	Fetal Muscle Leg	muscle
37	chr12:121290000-121293600	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr12:121290000-121300200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:121290000-121302600	Weak transcription	Liver	Liver
40	chr12:121290600-121293000	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr12:121290800-121292000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:121290800-121292000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:121290800-121292000	Enhancers	Psoas Muscle	Psoas
44	chr12:121290800-121292200	Enhancers	Primary T cells fromperipheralblood	blood
45	chr12:121290800-121292200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr12:121290800-121292400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:121290800-121292400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:121290800-121292600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:121290800-121294200	Enhancers	Left Ventricle	heart
50	chr12:121290800-121295200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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