Variant report

Variant	rs12623404
Chromosome Location	chr2:210317830-210317831
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	chr2:210287559..210290365-chr2:210315823..210318569,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000078018	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10153809	0.96[ASN][1000 genomes]
rs10174291	0.96[ASN][1000 genomes]
rs10182475	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs10185216	0.81[ASN][1000 genomes]
rs10198751	0.86[CEU][hapmap]
rs10200389	0.96[ASN][1000 genomes]
rs10200539	0.96[ASN][1000 genomes]
rs10210266	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10932297	0.91[ASN][1000 genomes]
rs10932301	0.96[ASN][1000 genomes]
rs11678209	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11889366	0.91[ASN][1000 genomes]
rs11900413	0.95[ASN][1000 genomes]
rs11904626	0.96[ASN][1000 genomes]
rs12613165	1.00[JPT][hapmap]
rs12614926	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12614974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12615372	0.88[CEU][hapmap]
rs12616589	0.88[CEU][hapmap]
rs12617330	0.94[ASN][1000 genomes]
rs12620654	0.88[CEU][hapmap]
rs12621534	0.94[ASN][1000 genomes]
rs12622130	0.94[ASN][1000 genomes]
rs12623555	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12694180	0.91[ASN][1000 genomes]
rs13005529	0.91[ASN][1000 genomes]
rs13023264	0.91[ASN][1000 genomes]
rs13024490	0.94[ASN][1000 genomes]
rs13028173	0.94[ASN][1000 genomes]
rs13028553	0.94[ASN][1000 genomes]
rs13033819	0.94[ASN][1000 genomes]
rs13034750	0.94[ASN][1000 genomes]
rs13391766	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13391768	0.89[ASN][1000 genomes]
rs1374333	0.94[ASN][1000 genomes]
rs1446593	1.00[JPT][hapmap]
rs1446596	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1509469	0.88[CEU][hapmap]
rs16842875	0.94[ASN][1000 genomes]
rs16842884	0.94[ASN][1000 genomes]
rs16843329	0.88[CEU][hapmap]
rs17236116	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2028893	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2123701	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2198478	0.88[CEU][hapmap]
rs2219085	0.88[CEU][hapmap]
rs2365657	0.88[CEU][hapmap]
rs2366112	0.88[CEU][hapmap]
rs2663649	0.88[CEU][hapmap]
rs2663651	0.88[CEU][hapmap]
rs2663653	0.88[CEU][hapmap]
rs2710477	0.86[CEU][hapmap]
rs2710479	0.88[CEU][hapmap]
rs28556312	0.96[ASN][1000 genomes]
rs28558587	0.92[ASN][1000 genomes]
rs28610349	0.96[ASN][1000 genomes]
rs288057	0.88[CEU][hapmap]
rs288065	0.88[CEU][hapmap]
rs288068	0.88[CEU][hapmap]
rs35424736	0.83[ASN][1000 genomes]
rs60358187	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6435528	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6435529	0.96[ASN][1000 genomes]
rs6733750	0.91[ASN][1000 genomes]
rs6751612	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6761283	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs72492734	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72995681	0.96[ASN][1000 genomes]
rs73060566	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7557610	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7563521	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7568431	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7568858	0.94[ASN][1000 genomes]
rs7569773	0.96[ASN][1000 genomes]
rs7575409	0.94[ASN][1000 genomes]
rs7577392	0.95[ASN][1000 genomes]
rs7593381	0.88[CEU][hapmap]
rs7594469	0.90[ASN][1000 genomes]
rs7594842	0.96[ASN][1000 genomes]
rs7595924	0.96[ASN][1000 genomes]
rs7602104	0.94[ASN][1000 genomes]
rs7608377	0.91[ASN][1000 genomes]
rs7608854	0.96[ASN][1000 genomes]
rs9288407	0.91[ASN][1000 genomes]
rs962475	0.88[CEU][hapmap]
rs992028	0.96[ASN][1000 genomes]
rs993784	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9967799	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	nsv834518	chr2:210204958-210372744	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv834519	chr2:210271017-210400153	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1005298	chr2:210277791-210318067	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12623404	LANCL1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:210306600-210337000	Weak transcription	Aorta	Aorta
2	chr2:210308600-210324200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:210312800-210322400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:210315600-210318200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:210315800-210318000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr2:210316000-210318200	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr2:210316000-210322400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:210316400-210319400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:210316400-210319600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:210316400-210327600	Weak transcription	Fetal Brain Male	brain
11	chr2:210316400-210328000	Weak transcription	Brain Germinal Matrix	brain
12	chr2:210316600-210318200	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr2:210316600-210322000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:210317000-210319600	Weak transcription	Fetal Brain Female	brain
15	chr2:210317200-210322400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:210317400-210318400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:210317400-210319400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:210317800-210318200	Enhancers	Pancreatic Islets	Pancreatic Islet

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