Variant report

Variant	rs300919
Chromosome Location	chr4:144264722-144264723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:144264296..144264969-chr6:30028972..30029813,2	Hela-S3	cervix:
2	chr4:144254658..144259448-chr4:144261105..144264742,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178972	Chromatin interaction
ENSG00000109458	Chromatin interaction
ENSG00000204623	Chromatin interaction
ENSG00000066379	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1027851	0.84[JPT][hapmap]
rs11100788	0.82[JPT][hapmap]
rs11947952	0.95[ASN][1000 genomes]
rs13123498	0.84[JPT][hapmap]
rs1472873	0.84[JPT][hapmap]
rs1510880	0.84[JPT][hapmap]
rs2013856	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2055730	0.84[JPT][hapmap]
rs300890	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs300891	0.94[ASN][1000 genomes]
rs300892	0.95[ASN][1000 genomes]
rs300893	0.80[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[ASN][1000 genomes]
rs300894	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs300895	0.80[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[ASN][1000 genomes]
rs300899	0.95[ASN][1000 genomes]
rs300901	0.90[ASN][1000 genomes]
rs300902	0.88[ASN][1000 genomes]
rs300903	0.91[ASN][1000 genomes]
rs300904	0.80[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs300905	0.80[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs300910	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs300911	0.96[CEU][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs300912	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs300913	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs300914	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs300915	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs300916	0.80[MEX][hapmap]
rs300917	0.81[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs300918	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3792652	0.84[JPT][hapmap]
rs3805247	0.84[JPT][hapmap]
rs3805249	0.83[JPT][hapmap]
rs3805251	0.82[JPT][hapmap]
rs3805253	0.84[JPT][hapmap]
rs3805254	0.84[JPT][hapmap]
rs3805256	0.84[JPT][hapmap]
rs3805257	0.84[JPT][hapmap]
rs3828512	0.84[JPT][hapmap]
rs3828513	0.84[JPT][hapmap]
rs568685	0.94[ASN][1000 genomes]
rs62337488	0.94[ASN][1000 genomes]
rs624170	0.95[ASN][1000 genomes]
rs624189	0.94[ASN][1000 genomes]
rs6537155	0.84[JPT][hapmap]
rs713140	0.84[JPT][hapmap]
rs719392	0.84[JPT][hapmap]
rs7680959	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033902	chr4:144114413-144285772	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1026110	chr4:144239825-144292148	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs300919	CLGN	cis	parietal	SCAN
rs300919	SLC10A7	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:144259200-144272400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:144259400-144265400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:144259400-144268600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr4:144259400-144272000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:144259400-144272600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr4:144259600-144265000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr4:144259600-144276200	Weak transcription	Fetal Kidney	kidney
8	chr4:144259800-144264800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr4:144259800-144264800	Weak transcription	Fetal Brain Female	brain
10	chr4:144259800-144265400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:144259800-144268600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr4:144260000-144267400	Weak transcription	Stomach Mucosa	stomach
13	chr4:144260000-144268600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:144260000-144272800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:144260200-144268600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:144261000-144265200	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr4:144261000-144265600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:144261000-144266000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr4:144261000-144268600	Weak transcription	Primary B cells from cord blood	blood
20	chr4:144261400-144265400	Weak transcription	HepG2	liver
21	chr4:144261600-144272600	Weak transcription	Adipose Nuclei	Adipose
22	chr4:144262400-144265400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:144262600-144264800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr4:144263000-144264800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr4:144263000-144264800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr4:144263000-144265200	Weak transcription	Fetal Intestine Large	intestine
27	chr4:144263000-144265200	Weak transcription	Right Ventricle	heart
28	chr4:144263000-144267400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr4:144263000-144267400	Weak transcription	Pancreas	Pancrea
30	chr4:144263000-144268600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr4:144263000-144276600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:144263000-144277800	Weak transcription	Fetal Thymus	thymus
33	chr4:144263400-144265200	Weak transcription	Brain Germinal Matrix	brain
34	chr4:144263600-144265400	Enhancers	Fetal Heart	heart
35	chr4:144263800-144265200	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr4:144263800-144266800	Enhancers	Placenta Amnion	Placenta Amnion
37	chr4:144264000-144264800	Enhancers	Brain Cingulate Gyrus	brain
38	chr4:144264000-144265200	Enhancers	Small Intestine	intestine
39	chr4:144264000-144265400	Enhancers	Brain Angular Gyrus	brain
40	chr4:144264000-144267600	Enhancers	Fetal Lung	lung
41	chr4:144264000-144270200	Enhancers	Rectal Smooth Muscle	rectum
42	chr4:144264000-144276400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:144264200-144264800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr4:144264200-144264800	Enhancers	Colonic Mucosa	Colon
45	chr4:144264200-144264800	Enhancers	Esophagus	oesophagus
46	chr4:144264200-144264800	Enhancers	Stomach Smooth Muscle	stomach
47	chr4:144264200-144265000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:144264200-144265000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:144264200-144265000	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr4:144264200-144265200	Flanking Active TSS	Brain Hippocampus Middle	brain

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