Variant report

Variant	rs1045300
Chromosome Location	chr2:112875039-112875040
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:112869211..112870960-chr2:112874200..112876971,2	K562	blood:
2	chr2:112874982..112878091-chr2:113030838..113033838,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188177	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10165845	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10175143	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10178449	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10182333	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10779884	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10864898	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.98[ASN][1000 genomes]
rs11675437	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12618637	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4241121	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4257409	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4613287	0.90[JPT][hapmap]
rs4848993	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs4849007	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849044	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6707397	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6730057	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731563	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6737707	0.90[JPT][hapmap]
rs7577442	0.95[ASN][1000 genomes]
rs7580507	0.98[ASN][1000 genomes]
rs7581849	1.00[JPT][hapmap]
rs7591702	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7595574	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9308669	0.89[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9653401	0.85[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9653422	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][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	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv1013218	chr2:112645633-112908416	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv3333591	chr2:112669320-112892618	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1014787	chr2:112679182-112908416	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv535893	chr2:112679182-112908416	Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1045300	POLR1B	cis	parietal	SCAN
rs1045300	POLR1B	cis	cerebellum	SCAN
rs1045300	FBLN7	cis	cerebellum	SCAN
rs1045300	CCDC138	cis	cerebellum	SCAN
rs1045300	FBLN7	cis	Artery Tibial	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112822800-112876800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr2:112835800-112883200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:112845400-112875200	Weak transcription	Right Ventricle	heart
4	chr2:112851200-112881600	Weak transcription	Stomach Mucosa	stomach
5	chr2:112856800-112875600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:112856800-112881800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:112857000-112883000	Weak transcription	Hela-S3	cervix
8	chr2:112857000-112891200	Weak transcription	Small Intestine	intestine
9	chr2:112857200-112877600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:112859600-112877200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:112866200-112879000	Weak transcription	Psoas Muscle	Psoas
12	chr2:112867200-112877200	Weak transcription	Brain Substantia Nigra	brain
13	chr2:112867200-112880400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:112867600-112882600	Weak transcription	Fetal Stomach	stomach
15	chr2:112867800-112879800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:112867800-112881400	Weak transcription	Fetal Intestine Small	intestine
17	chr2:112868600-112877200	Weak transcription	Fetal Brain Female	brain
18	chr2:112868800-112875400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:112869800-112884000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:112869800-112890200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:112870000-112875200	Weak transcription	Dnd41	blood
22	chr2:112870000-112877000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr2:112870000-112880200	Weak transcription	Fetal Heart	heart
24	chr2:112870000-112881800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:112870200-112877400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr2:112870400-112875200	Weak transcription	K562	blood
27	chr2:112870400-112876000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:112870400-112876000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:112870400-112880000	Weak transcription	HSMMtube	muscle
30	chr2:112870400-112880200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:112870400-112880200	Weak transcription	Fetal Kidney	kidney
32	chr2:112870400-112880200	Weak transcription	Pancreas	Pancrea
33	chr2:112870400-112880200	Weak transcription	Thymus	Thymus
34	chr2:112870400-112895000	Weak transcription	HMEC	breast
35	chr2:112870400-112895200	Weak transcription	Gastric	stomach
36	chr2:112870600-112875200	Weak transcription	Brain Anterior Caudate	brain
37	chr2:112870600-112875400	Weak transcription	Spleen	Spleen
38	chr2:112870600-112879600	Weak transcription	Fetal Lung	lung
39	chr2:112870600-112882000	Weak transcription	Esophagus	oesophagus
40	chr2:112870600-112882200	Weak transcription	NHEK	skin
41	chr2:112870600-112882800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr2:112871000-112875400	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:112871000-112877200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr2:112871000-112877600	Weak transcription	Colonic Mucosa	Colon
45	chr2:112871000-112879600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:112871000-112879600	Weak transcription	A549	lung
47	chr2:112871200-112875200	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:112871200-112875400	Weak transcription	Ovary	ovary
49	chr2:112871200-112875600	Weak transcription	HUVEC	blood vessel
50	chr2:112871200-112877400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links