Variant report

Variant	rs2396999
Chromosome Location	chr5:154114114-154114115
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:154110904..154115503-chr5:154133051..154136642,5	MCF-7	breast:
2	chr5:154110340..154114557-chr5:154119062..154122333,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155506	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1035368	0.93[CEU][hapmap];0.89[YRI][hapmap]
rs12188828	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs12300	0.81[CEU][hapmap]
rs1233078	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17116409	0.86[CHB][hapmap]
rs17116411	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs17116414	0.90[EUR][1000 genomes]
rs17116421	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs17116442	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs17116534	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs1974776	0.93[CEU][hapmap]
rs1974777	0.93[CEU][hapmap]
rs2042168	0.93[CEU][hapmap]
rs2112223	0.93[CEU][hapmap]
rs2161128	0.93[CEU][hapmap]
rs2258437	0.87[CEU][hapmap]
rs2544874	0.81[EUR][1000 genomes]
rs2544875	0.81[EUR][1000 genomes]
rs2544876	0.81[EUR][1000 genomes]
rs2544880	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs2644743	0.93[CEU][hapmap];0.89[YRI][hapmap]
rs2644744	0.93[CEU][hapmap]
rs2688186	0.81[EUR][1000 genomes]
rs2688187	0.81[EUR][1000 genomes]
rs2688188	0.81[EUR][1000 genomes]
rs2688189	0.81[EUR][1000 genomes]
rs2688190	0.81[EUR][1000 genomes]
rs2688191	0.81[EUR][1000 genomes]
rs2688198	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs2688200	0.81[EUR][1000 genomes]
rs2688201	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs2688206	0.81[EUR][1000 genomes]
rs2688208	0.93[CEU][hapmap]
rs348739	0.93[CEU][hapmap];0.89[YRI][hapmap]
rs39614	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs4623203	0.88[ASN][1000 genomes]
rs4626377	0.81[ASN][1000 genomes]
rs56374414	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58415346	0.90[EUR][1000 genomes]
rs59525998	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59749917	0.97[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6876004	0.88[ASN][1000 genomes]
rs6884416	0.83[EUR][1000 genomes]
rs702742	0.93[CEU][hapmap];0.92[YRI][hapmap];0.83[EUR][1000 genomes]
rs73276742	0.90[EUR][1000 genomes]
rs7723269	0.90[EUR][1000 genomes]
rs7728194	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs816717	0.93[CEU][hapmap];0.82[YRI][hapmap];0.88[EUR][1000 genomes]
rs816718	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs816720	0.93[CEU][hapmap]
rs816722	0.81[EUR][1000 genomes]
rs9942412	0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021153	chr5:154099869-154147970	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154074200-154120000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:154102200-154117400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr5:154104000-154120000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr5:154104400-154118600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr5:154104600-154117600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:154107200-154133200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr5:154108800-154117400	Weak transcription	Pancreas	Pancrea
8	chr5:154109200-154120000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:154109600-154117400	Weak transcription	A549	lung
10	chr5:154109600-154120000	Weak transcription	Liver	Liver
11	chr5:154109600-154120800	Weak transcription	Stomach Mucosa	stomach
12	chr5:154111200-154120400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr5:154111400-154117400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:154111400-154120200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr5:154112000-154120800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr5:154112200-154123600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:154112600-154120200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr5:154112800-154117400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr5:154113000-154117200	Weak transcription	HepG2	liver
20	chr5:154113000-154120400	Weak transcription	Psoas Muscle	Psoas
21	chr5:154114000-154114400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr5:154114000-154115000	Enhancers	Primary monocytes fromperipheralblood	blood

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