Variant report

Variant	rs12025368
Chromosome Location	chr1:171847295-171847296
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	chr1:171840991..171843556-chr1:171846229..171848483,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1015009	0.93[ASN][1000 genomes]
rs1015010	0.93[ASN][1000 genomes]
rs10436867	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10737340	0.86[CHB][hapmap]
rs10798687	0.93[ASN][1000 genomes]
rs10798688	0.91[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs10798690	0.93[ASN][1000 genomes]
rs10798691	0.93[ASN][1000 genomes]
rs10798692	0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs10798693	0.91[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs10798712	0.86[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798751	0.86[CHB][hapmap]
rs10913811	0.93[ASN][1000 genomes]
rs10913812	0.93[ASN][1000 genomes]
rs10913814	0.93[ASN][1000 genomes]
rs11579330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12028585	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12048200	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555384	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2145382	0.86[CHB][hapmap]
rs2294723	0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs2294724	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2901603	0.86[CHB][hapmap]
rs6425438	0.92[CEU][hapmap]
rs6425481	0.86[CHB][hapmap]
rs6425482	0.86[CHB][hapmap]
rs72711798	0.83[ASN][1000 genomes]
rs72713710	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72713711	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7518914	0.85[CHB][hapmap]
rs7538839	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7546406	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv831893	chr1:171802450-171985000	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12025368	DNM3	cis	cerebellum	SCAN
rs12025368	RC3H1	cis	cerebellum	SCAN
rs12025368	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL
rs12025368	MYOC	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171828400-171850800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:171838800-171848200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:171844400-171847800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr1:171844400-171858200	Weak transcription	Left Ventricle	heart
5	chr1:171846600-171847800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:171846600-171847800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:171846600-171847800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:171846800-171847600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:171846800-171847600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr1:171846800-171850600	Weak transcription	Fetal Intestine Small	intestine
11	chr1:171847000-171848200	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:171847000-171848800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:171847000-171850600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:171847000-171850600	Weak transcription	HSMMtube	muscle
15	chr1:171847200-171848200	Weak transcription	Brain Angular Gyrus	brain
16	chr1:171847200-171848200	Weak transcription	Brain Substantia Nigra	brain
17	chr1:171847200-171849000	Weak transcription	Brain Anterior Caudate	brain
18	chr1:171847200-171850600	Weak transcription	Brain Cingulate Gyrus	brain

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