Variant report

Variant	rs1880183
Chromosome Location	chr4:69190493-69190494
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:69190188..69191856-chr4:69197482..69199638,2	MCF-7	breast:
2	chr4:69188150..69190673-chr4:69212848..69214663,2	K562	blood:
3	chr4:69188337..69192029-chr4:69196790..69201126,5	K562	blood:
4	chr4:69184387..69189149-chr4:69189998..69193594,6	K562	blood:
5	chr4:69188491..69190589-chr4:69207832..69210150,2	K562	blood:
6	chr4:69188337..69191371-chr4:69197664..69201126,3	K562	blood:

Variant related genes	Relation type
ENSG00000083896	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10005832	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10471153	0.95[EUR][1000 genomes]
rs10866204	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11131746	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs11732554	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11735530	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13121372	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13127027	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13148330	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1320797	1.00[ASN][1000 genomes]
rs1406695	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1406696	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17089240	0.94[CEU][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17089241	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1715086	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1730872	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1730875	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1919905	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1962172	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2140519	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2319887	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34032921	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34186169	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34223548	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34265565	0.85[EUR][1000 genomes]
rs34282559	1.00[ASN][1000 genomes]
rs34474886	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34527218	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34896019	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35051311	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797007	0.86[ASN][1000 genomes]
rs3927373	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4860292	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4860927	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4860928	1.00[ASN][1000 genomes]
rs4860930	0.91[ASN][1000 genomes]
rs4860932	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4860933	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4860934	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4860935	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62316204	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6552179	0.95[ASN][1000 genomes]
rs6822778	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7658151	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7671950	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7672364	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7696268	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs953794	0.80[EUR][1000 genomes]
rs953795	0.80[EUR][1000 genomes]
rs9990842	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9991215	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008084	chr4:68797598-69482831	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv537131	chr4:68797598-69482831	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1806586	chr4:68943858-69592846	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv461546	chr4:69049643-69223057	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv594506	chr4:69049643-69223057	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv537132	chr4:69149648-69482831	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	esv2757061	chr4:69178920-69631668	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1880183	YTHDC1	Cis_1M	lymphoblastoid	RTeQTL
rs1880183	UTP3	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69176200-69203600	Strong transcription	Liver	Liver
2	chr4:69176200-69203600	Strong transcription	HSMM	muscle
3	chr4:69176200-69204000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:69176200-69204200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr4:69176400-69203800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:69176400-69204000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:69176400-69204400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:69176400-69204600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:69176600-69198400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr4:69176600-69203600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:69176600-69204600	Strong transcription	Fetal Thymus	thymus
12	chr4:69176800-69202200	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr4:69176800-69203600	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr4:69177200-69203600	Strong transcription	Placenta	Placenta
15	chr4:69177200-69203800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:69177200-69204200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:69177400-69204000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr4:69177800-69201200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr4:69177800-69203800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr4:69178000-69190600	Strong transcription	HUVEC	blood vessel
21	chr4:69178000-69203600	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr4:69178000-69205000	Strong transcription	Dnd41	blood
23	chr4:69178200-69193200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr4:69179200-69194200	Weak transcription	Hela-S3	cervix
25	chr4:69179200-69198600	Strong transcription	NHEK	skin
26	chr4:69180600-69194400	Weak transcription	Psoas Muscle	Psoas
27	chr4:69182600-69192000	Weak transcription	Fetal Heart	heart
28	chr4:69182600-69213200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr4:69182800-69207200	Weak transcription	Small Intestine	intestine
30	chr4:69182800-69209200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:69183000-69197800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr4:69183000-69198600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:69183000-69207800	Weak transcription	Esophagus	oesophagus
34	chr4:69183400-69200600	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr4:69183600-69204200	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr4:69183600-69204200	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr4:69183800-69203600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr4:69183800-69204200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr4:69184200-69192400	Weak transcription	Pancreas	Pancrea
40	chr4:69184200-69204200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:69184200-69204200	Weak transcription	Gastric	stomach
42	chr4:69184200-69207800	Weak transcription	Spleen	Spleen
43	chr4:69184200-69212200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr4:69184200-69212800	Weak transcription	Aorta	Aorta
45	chr4:69184400-69194600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr4:69184800-69204200	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr4:69185200-69203800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr4:69185400-69192000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr4:69185400-69194600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr4:69185400-69203800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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