Variant report

Variant	rs845452
Chromosome Location	chr1:210417861-210417862
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210417526..210420172-chr1:210543053..210546033,2	MCF-7	breast:
2	chr1:210417487..210419206-chr1:210423476..210426436,2	MCF-7	breast:
3	chr1:210417610..210419303-chr1:210546135..210547707,2	K562	blood:
4	chr1:210417610..210419697-chr1:210545782..210547707,3	K562	blood:

Variant related genes	Relation type
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10489385	1.00[ASW][hapmap]
rs10489391	0.92[AMR][1000 genomes]
rs10863818	0.90[AMR][1000 genomes]
rs11119455	0.90[AMR][1000 genomes]
rs11119456	0.82[AMR][1000 genomes]
rs12067807	0.82[ASN][1000 genomes]
rs12069380	0.84[AMR][1000 genomes]
rs12069491	0.82[AMR][1000 genomes]
rs12070628	0.81[AMR][1000 genomes]
rs12083219	0.82[ASN][1000 genomes]
rs12138216	0.84[TSI][hapmap]
rs2273047	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs4844987	0.90[AMR][1000 genomes]
rs4844988	0.84[AMR][1000 genomes]
rs4844989	0.92[AMR][1000 genomes]
rs583148	0.83[AMR][1000 genomes]
rs587203	0.90[TSI][hapmap];0.84[AMR][1000 genomes]
rs588197	0.90[TSI][hapmap];0.83[AMR][1000 genomes]
rs590380	0.90[TSI][hapmap];0.83[AMR][1000 genomes]
rs608791	0.90[TSI][hapmap];0.83[AMR][1000 genomes]
rs614167	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs628423	0.84[AMR][1000 genomes]
rs628869	0.84[AMR][1000 genomes]
rs628908	0.91[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs634601	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs645311	0.84[AMR][1000 genomes]
rs645890	0.83[AMR][1000 genomes]
rs650728	1.00[ASW][hapmap];0.82[CEU][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs652241	0.83[AMR][1000 genomes]
rs652256	0.83[AMR][1000 genomes]
rs661190	0.81[AMR][1000 genomes]
rs662424	0.82[AMR][1000 genomes]
rs664072	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs664097	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs672819	0.84[EUR][1000 genomes]
rs689248	0.90[TSI][hapmap];0.83[AMR][1000 genomes]
rs701941	0.83[EUR][1000 genomes]
rs701942	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs701943	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs701944	1.00[ASW][hapmap];0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7416285	0.82[ASN][1000 genomes]
rs815358	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs845455	1.00[ASW][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]

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	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs845452	CR1	cis	parietal	SCAN
rs845452	SYT14	cis	parietal	SCAN
rs845452	SLC30A1	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210407800-210424000	Weak transcription	Colonic Mucosa	Colon
2	chr1:210407800-210424000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:210407800-210424200	Weak transcription	Pancreas	Pancrea
4	chr1:210408000-210418200	Weak transcription	Esophagus	oesophagus
5	chr1:210408000-210424000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:210410800-210424000	Weak transcription	Lung	lung
7	chr1:210410800-210424200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:210411200-210423600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:210411400-210423800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:210411600-210418000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:210411600-210418400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:210411800-210422200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:210411800-210423600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:210411800-210423600	Weak transcription	Brain Anterior Caudate	brain
15	chr1:210411800-210423800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:210412000-210422800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:210412000-210423800	Weak transcription	Brain Angular Gyrus	brain
18	chr1:210413800-210418200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:210414000-210418000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:210414000-210421400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:210414000-210424000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:210414000-210424200	Weak transcription	Aorta	Aorta
23	chr1:210414000-210424400	Weak transcription	Ovary	ovary
24	chr1:210414400-210419600	Weak transcription	HUVEC	blood vessel
25	chr1:210414400-210424000	Weak transcription	NHEK	skin
26	chr1:210414800-210418000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:210414800-210421400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:210414800-210423800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:210415000-210424000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:210415200-210423800	Weak transcription	Colon Smooth Muscle	Colon
31	chr1:210415400-210423800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:210415600-210422800	Weak transcription	Fetal Stomach	stomach
33	chr1:210415600-210423200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:210415800-210424000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:210416000-210421600	Weak transcription	Fetal Muscle Leg	muscle
36	chr1:210416200-210424000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr1:210416800-210418000	Enhancers	NH-A	brain
38	chr1:210417600-210418800	Enhancers	HMEC	breast
39	chr1:210417600-210418800	Bivalent Enhancer	Osteobl	bone
40	chr1:210417600-210419000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:210417600-210419200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:210417600-210419200	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr1:210417600-210419200	Enhancers	Muscle Satellite Cultured Cells	--
44	chr1:210417600-210420600	Enhancers	HSMM	muscle
45	chr1:210417800-210418000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:210417800-210418600	Enhancers	NHDF-Ad	bronchial
47	chr1:210417800-210419800	Enhancers	HSMMtube	muscle

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