Variant report

Variant	rs1555381
Chromosome Location	chr1:172008479-172008480
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	chr1:171999936..172003512-chr1:172007617..172010205,3	K562	blood:
2	chr1:172008308..172011065-chr1:172384057..172386802,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135845	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10752864	0.96[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs10797689	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10911004	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12029864	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12075807	0.89[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[ASN][1000 genomes]
rs12091015	0.90[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[ASN][1000 genomes]
rs12760234	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2104037	0.88[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2819525	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2819527	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819530	0.83[JPT][hapmap]
rs35665317	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4075021	0.96[CEU][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs484686	0.87[ASW][hapmap]
rs495590	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6670207	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6671218	0.84[EUR][1000 genomes]
rs6676154	0.86[EUR][1000 genomes]
rs9425847	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9659615	0.82[ASN][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	nsv532342	chr1:171922237-172133785	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
2	nsv3532	chr1:171997451-172042351	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1555381	POU2F1	cis	parietal	SCAN
rs1555381	C1orf112	cis	cerebellum	SCAN
rs1555381	MPZL1	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171994000-172020400	Weak transcription	Left Ventricle	heart
2	chr1:171994200-172009000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:172000000-172012800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:172000400-172009800	Weak transcription	Brain Angular Gyrus	brain
5	chr1:172000600-172013600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:172000800-172011400	Weak transcription	Right Ventricle	heart
7	chr1:172000800-172013800	Weak transcription	Fetal Brain Female	brain
8	chr1:172001400-172019000	Weak transcription	Fetal Brain Male	brain
9	chr1:172002200-172011600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:172002800-172013200	Weak transcription	Primary T cells from cord blood	blood
11	chr1:172003000-172012400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:172003200-172009800	Weak transcription	Brain Anterior Caudate	brain
13	chr1:172004000-172014000	Weak transcription	Lung	lung
14	chr1:172004200-172008800	Weak transcription	NHEK	skin
15	chr1:172005600-172015200	Weak transcription	HSMMtube	muscle
16	chr1:172006000-172013800	Weak transcription	Brain Germinal Matrix	brain
17	chr1:172006400-172010200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:172006400-172025600	Weak transcription	Adipose Nuclei	Adipose
19	chr1:172006800-172010800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:172007000-172009800	Weak transcription	Aorta	Aorta
21	chr1:172007000-172010600	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr1:172007200-172009800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:172007600-172008600	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:172007600-172014000	Weak transcription	Brain Substantia Nigra	brain
25	chr1:172007600-172014800	Weak transcription	Thymus	Thymus
26	chr1:172008200-172011000	Weak transcription	Ovary	ovary
27	chr1:172008400-172008800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:172008400-172013200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links