Variant report

Variant	rs550892
Chromosome Location	chr1:93584199-93584200
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	chr1:93584109-93584241	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93582432..93585067-chr1:93594347..93596208,2	K562	blood:

Variant related genes	Relation type
MTF2	TF binding region
ENSG00000143033	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11164869	0.93[CEU][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12062154	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12080248	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12736775	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17131705	1.00[CHD][hapmap]
rs17131710	1.00[CHD][hapmap]
rs2391228	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2749734	0.95[ASN][1000 genomes]
rs2765545	0.82[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[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs475120	1.00[CHD][hapmap]
rs488345	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs490153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs495580	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs500349	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs502651	0.90[ASN][1000 genomes]
rs519319	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs539544	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs546445	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs548751	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs566843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580828	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6670960	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696026	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6702666	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6703169	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7555395	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs550892	RP4-717I23.3	cis	Artery Aorta	GTEx
rs550892	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs550892	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs550892	CCDC18	Cis_1M	lymphoblastoid	RTeQTL
rs550892	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs550892	TMED5	cis	parietal	SCAN
rs550892	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs550892	RP4-717I23.3	cis	Thyroid	GTEx
rs550892	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs550892	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs550892	TMED5	cis	cerebellum	SCAN
rs550892	RP4-717I23.3	cis	lung	GTEx
rs550892	RP4-717I23.3	cis	Whole Blood	GTEx
rs550892	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs550892	RP4-717I23.3	cis	Artery Tibial	GTEx
rs550892	RP4-717I23.3	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93546200-93602200	Weak transcription	Aorta	Aorta
2	chr1:93547600-93600000	Weak transcription	HSMMtube	muscle
3	chr1:93548000-93601800	Weak transcription	NHLF	lung
4	chr1:93565200-93625200	Weak transcription	Stomach Mucosa	stomach
5	chr1:93568400-93584200	Weak transcription	Fetal Brain Male	brain
6	chr1:93571400-93602200	Weak transcription	Colonic Mucosa	Colon
7	chr1:93572400-93599600	Weak transcription	Spleen	Spleen
8	chr1:93573400-93627000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:93573600-93586000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:93573800-93609000	Strong transcription	Fetal Thymus	thymus
11	chr1:93574200-93609000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:93574600-93584800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:93574600-93585800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:93574600-93609000	Strong transcription	Dnd41	blood
15	chr1:93574600-93630200	Weak transcription	Right Ventricle	heart
16	chr1:93575200-93589800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:93575800-93589200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:93577200-93592800	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:93577200-93597000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:93577600-93585200	Strong transcription	Primary hematopoietic stem cells	blood
21	chr1:93577600-93586600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:93577600-93586800	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:93577600-93588800	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:93577600-93591400	Weak transcription	Fetal Heart	heart
25	chr1:93577800-93601600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:93578200-93587200	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr1:93578200-93588200	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:93578400-93587400	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr1:93578400-93587600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:93578600-93586600	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr1:93578600-93586800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:93578600-93586800	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:93578800-93613600	Weak transcription	Psoas Muscle	Psoas
34	chr1:93578800-93620600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:93579600-93586800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:93579600-93587200	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr1:93579600-93595400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:93579800-93586600	Strong transcription	Liver	Liver
39	chr1:93579800-93587200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr1:93579800-93588000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:93580000-93585800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:93580000-93586400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:93580000-93587600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr1:93580000-93587600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:93580000-93588200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:93580000-93624000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr1:93580200-93586600	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr1:93580200-93643600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:93580400-93585600	Strong transcription	Fetal Lung	lung
50	chr1:93580400-93585800	Strong transcription	Primary T cells from cord blood	blood

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