Variant report

Variant	rs1233078
Chromosome Location	chr5:154111128-154111129
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:154110905..154113658-chr5:154115754..154117502,2	K562	blood:
2	chr5:154110904..154115503-chr5:154133051..154136642,5	MCF-7	breast:
3	chr5:154110340..154114557-chr5:154119062..154122333,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155506	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2396999	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2544860	0.91[CEU][hapmap];0.82[YRI][hapmap]
rs4623203	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6873483	0.86[AFR][1000 genomes]
rs6876004	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7728194	0.86[ASN][1000 genomes]
rs816747	0.91[ASW][hapmap];0.91[CEU][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap]
rs960499	1.00[ASW][hapmap];0.91[CEU][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.83[EUR][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	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
2	nsv964965	chr5:154108820-154112255	Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1233078	TIMD4	cis	cerebellum	SCAN
rs1233078	LARP1	cis	Whole Blood	GTEx

Chromatin state (count:21 , 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	chr5:154108600-154112800	Weak transcription	Psoas Muscle	Psoas
8	chr5:154108800-154117400	Weak transcription	Pancreas	Pancrea
9	chr5:154109200-154120000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:154109600-154117400	Weak transcription	A549	lung
11	chr5:154109600-154120000	Weak transcription	Liver	Liver
12	chr5:154109600-154120800	Weak transcription	Stomach Mucosa	stomach
13	chr5:154109800-154111800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr5:154110400-154112000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:154110800-154111200	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr5:154110800-154111200	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr5:154110800-154111400	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr5:154110800-154113000	Enhancers	HepG2	liver
19	chr5:154111000-154111400	Enhancers	H1 Cell Line	embryonic stem cell
20	chr5:154111000-154111400	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr5:154111000-154111400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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