Variant report

Variant	rs12080248
Chromosome Location	chr1:93606230-93606231
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93604940..93607069-chr1:93611441..93613644,2	K562	blood:
2	chr1:93605569..93607505-chr1:93611441..93613636,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11164869	0.94[CEU][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12062154	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12736775	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391228	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2749734	0.95[ASN][1000 genomes]
rs2765545	0.84[YRI][hapmap]
rs2785602	1.00[ASN][1000 genomes]
rs2785605	1.00[ASN][1000 genomes]
rs2815419	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2815423	1.00[ASN][1000 genomes]
rs2815424	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs488345	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs490153	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs495580	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs500349	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs502651	0.90[ASN][1000 genomes]
rs519319	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs539544	1.00[ASN][1000 genomes]
rs546445	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs548751	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs550892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566843	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580828	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6670960	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6702666	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6703169	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7555395	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs797594	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs12080248	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12080248	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs12080248	RP4-717I23.3	cis	Whole Blood	GTEx
rs12080248	RP4-717I23.3	cis	lung	GTEx
rs12080248	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs12080248	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs12080248	CCDC18	Cis_1M	lymphoblastoid	RTeQTL
rs12080248	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs12080248	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs12080248	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs12080248	RP4-717I23.3	cis	Thyroid	GTEx
rs12080248	RP4-717I23.3	cis	Artery Tibial	GTEx
rs12080248	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs12080248	RP4-717I23.3	cis	Artery Aorta	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93565200-93625200	Weak transcription	Stomach Mucosa	stomach
2	chr1:93573400-93627000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:93573800-93609000	Strong transcription	Fetal Thymus	thymus
4	chr1:93574200-93609000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:93574600-93609000	Strong transcription	Dnd41	blood
6	chr1:93574600-93630200	Weak transcription	Right Ventricle	heart
7	chr1:93578800-93613600	Weak transcription	Psoas Muscle	Psoas
8	chr1:93578800-93620600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:93580000-93624000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:93580200-93643600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:93581200-93616800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:93582400-93620400	Weak transcription	Small Intestine	intestine
13	chr1:93582400-93642800	Weak transcription	Gastric	stomach
14	chr1:93583200-93628800	Weak transcription	Brain Angular Gyrus	brain
15	chr1:93583600-93613800	Weak transcription	Lung	lung
16	chr1:93583600-93623800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:93583600-93635400	Weak transcription	Pancreas	Pancrea
18	chr1:93585200-93609200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:93585800-93642200	Weak transcription	Esophagus	oesophagus
20	chr1:93586200-93623400	Weak transcription	Fetal Brain Male	brain
21	chr1:93586800-93621000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:93590200-93608600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:93591200-93607000	Strong transcription	Primary hematopoietic stem cells	blood
24	chr1:93591200-93612600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:93591400-93607000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:93591400-93616600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:93592000-93608800	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:93592000-93609200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:93592200-93609000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:93592400-93607000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:93592600-93606800	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr1:93592600-93606800	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr1:93592600-93607200	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr1:93592600-93608600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:93592600-93609000	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:93592600-93609000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:93593000-93614200	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:93594400-93606800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr1:93594400-93611400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:93595000-93609200	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:93595400-93612400	Weak transcription	Fetal Heart	heart
42	chr1:93595800-93609200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:93595800-93635600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:93596800-93606800	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr1:93597400-93625400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr1:93598600-93608200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:93598800-93609200	Strong transcription	HSMM	muscle
48	chr1:93599800-93606600	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr1:93600400-93635400	Weak transcription	Spleen	Spleen
50	chr1:93601000-93643600	Weak transcription	HSMMtube	muscle

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