Variant report

Variant	rs28404345
Chromosome Location	chr4:100855322-100855323
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:100850716..100855335-chr4:100865818..100872882,15	K562	blood:
2	chr4:100854185..100858103-chr4:100869055..100872773,4	MCF-7	breast:
3	chr4:100855120..100857614-chr4:100862703..100864671,2	K562	blood:
4	chr4:100830733..100833112-chr4:100854057..100856497,2	K562	blood:

Variant related genes	Relation type
ENSG00000245322	Chromatin interaction
ENSG00000164032	Chromatin interaction
ENSG00000164031	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10026048	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11732776	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11935024	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11935399	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1365492	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs17029583	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1896166	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1961323	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2098937	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2114442	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2298735	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2866174	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2866180	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28706589	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756087	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3775511	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs60978748	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6532835	0.96[ASN][1000 genomes]
rs6532836	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6811559	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6848337	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6849599	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6854536	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7675947	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7676564	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7684872	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7686428	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689566	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7692416	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs919132	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs919133	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9307242	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][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	nsv879661	chr4:100805207-100869635	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv879662	chr4:100849466-100876648	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28404345	DAPP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100816000-100867000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:100816000-100867000	Weak transcription	Lung	lung
3	chr4:100816200-100866200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:100820000-100866200	Weak transcription	Fetal Heart	heart
5	chr4:100824000-100865800	Weak transcription	Psoas Muscle	Psoas
6	chr4:100824400-100866000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr4:100827600-100856400	Weak transcription	Brain Substantia Nigra	brain
8	chr4:100828800-100866200	Weak transcription	Stomach Mucosa	stomach
9	chr4:100829200-100856400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:100829200-100866600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:100829400-100856200	Weak transcription	HepG2	liver
12	chr4:100829600-100866200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr4:100836600-100856800	Weak transcription	Spleen	Spleen
14	chr4:100839200-100855600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:100839200-100857400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:100840000-100862600	Weak transcription	K562	blood
17	chr4:100840200-100864600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr4:100840200-100865800	Weak transcription	Ovary	ovary
19	chr4:100840200-100866000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr4:100840200-100867000	Weak transcription	Gastric	stomach
21	chr4:100840400-100856400	Weak transcription	Fetal Kidney	kidney
22	chr4:100840400-100856400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr4:100840400-100856800	Weak transcription	Thymus	Thymus
24	chr4:100840400-100864600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:100840400-100866800	Weak transcription	Aorta	Aorta
26	chr4:100840400-100867000	Weak transcription	Esophagus	oesophagus
27	chr4:100840600-100862200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr4:100840800-100855600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:100840800-100858200	Weak transcription	Fetal Stomach	stomach
30	chr4:100843400-100856200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr4:100844200-100856400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr4:100844800-100856400	Weak transcription	NH-A	brain
33	chr4:100847600-100856400	Weak transcription	Brain Angular Gyrus	brain
34	chr4:100847800-100856400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:100847800-100864600	Weak transcription	Hela-S3	cervix
36	chr4:100847800-100866200	Weak transcription	HSMMtube	muscle
37	chr4:100848400-100856600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr4:100848400-100866200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr4:100849600-100864800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr4:100849800-100856400	Weak transcription	Osteobl	bone
41	chr4:100850400-100856400	Weak transcription	Primary T cells from cord blood	blood
42	chr4:100850400-100864800	Weak transcription	HUVEC	blood vessel
43	chr4:100850600-100856400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr4:100850600-100856400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:100850600-100856400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:100851000-100856200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr4:100851000-100856200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:100851800-100855600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr4:100851800-100856000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr4:100851800-100856200	Weak transcription	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links