Variant report

Variant	rs3845404
Chromosome Location	chr1:180564536-180564537
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180557727..180561023-chr1:180561161..180564743,6	K562	blood:
2	chr1:180552650..180554961-chr1:180564277..180566227,2	K562	blood:
3	chr1:180563913..180566182-chr1:180599557..180601195,2	K562	blood:
4	chr1:180550479..180555497-chr1:180560043..180567544,7	K562	blood:
5	chr1:180563278..180564789-chr1:180567312..180569101,2	K562	blood:
6	chr1:180558143..180561068-chr1:180562367..180566154,4	K562	blood:

Variant related genes	Relation type
ENSG00000143324	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10494530	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10737347	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10737348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10753220	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10753221	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10798780	0.80[ASN][1000 genomes]
rs10798781	0.80[ASN][1000 genomes]
rs10798784	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3845403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856052	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3856055	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3915573	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4111062	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4111063	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4111064	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4144583	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5020729	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7519155	0.95[CHB][hapmap]
rs7521872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7544326	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7551817	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554099	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv825520	chr1:180562677-180564787	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3845404	KIAA0241	trans	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180561600-180564800	Enhancers	Pancreas	Pancrea
2	chr1:180562000-180564800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:180562200-180564600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:180562200-180564800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr1:180562200-180565000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:180563600-180564800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:180563600-180567200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:180563800-180564800	Enhancers	A549	lung
9	chr1:180564200-180564600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:180564200-180564800	Enhancers	Right Atrium	heart
11	chr1:180564200-180567600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:180564400-180564800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:180564400-180564800	Enhancers	K562	blood
14	chr1:180564400-180566200	Weak transcription	Fetal Brain Female	brain
15	chr1:180564400-180572800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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