Variant report

Variant	rs28402205
Chromosome Location	chr4:53518133-53518134
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:53511997..53515901-chr4:53517451..53520031,4	K562	blood:
2	chr4:53515781..53522890-chr4:53523068..53527068,15	MCF-7	breast:
3	chr4:53516922..53519099-chr4:53521219..53522801,2	K562	blood:
4	chr4:53512951..53517054-chr4:53517581..53520701,5	K562	blood:
5	chr4:53514631..53516168-chr4:53516292..53518256,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248866	Chromatin interaction
ENSG00000109189	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10000311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10001085	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10001370	0.87[ASN][1000 genomes]
rs10001387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10002261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10003396	0.87[ASN][1000 genomes]
rs10010306	0.93[ASN][1000 genomes]
rs10012676	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10014752	1.00[ASN][1000 genomes]
rs10014850	0.94[ASN][1000 genomes]
rs10020568	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10021143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10023867	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10027906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10028085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10028755	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10029145	0.93[ASN][1000 genomes]
rs10031386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10032700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10033218	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10471216	1.00[ASN][1000 genomes]
rs13434726	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13435157	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28376189	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28379922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28380682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28396506	1.00[AMR][1000 genomes]
rs28411005	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28412170	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28430452	1.00[ASN][1000 genomes]
rs28451750	0.93[ASN][1000 genomes]
rs28475600	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28478374	1.00[AMR][1000 genomes]
rs28482298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28503210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28565016	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28588481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28590396	1.00[ASN][1000 genomes]
rs28619184	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28644292	0.93[ASN][1000 genomes]
rs28654693	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28660550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28660571	1.00[ASN][1000 genomes]
rs28672279	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28694544	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28721897	1.00[ASN][1000 genomes]
rs28722174	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28784684	1.00[ASN][1000 genomes]
rs28825181	0.90[ASN][1000 genomes]
rs28825412	1.00[ASN][1000 genomes]
rs28849759	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28852068	1.00[ASN][1000 genomes]
rs6830833	1.00[ASN][1000 genomes]
rs7673679	0.90[ASN][1000 genomes]
rs9990686	1.00[ASN][1000 genomes]
rs9994643	1.00[ASN][1000 genomes]
rs9997863	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1000931	chr4:53420849-53689319	Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537093	chr4:53420849-53689319	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv948860	chr4:53421172-53675549	Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv2754049	chr4:53454272-53539672	Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv524494	chr4:53459620-53582065	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53464200-53523600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:53496600-53522800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr4:53506600-53521200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:53507600-53522000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:53508000-53523800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:53508400-53523800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:53508600-53522400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:53509600-53523800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:53510000-53518200	Weak transcription	Fetal Intestine Small	intestine
10	chr4:53510000-53518400	Weak transcription	Brain Germinal Matrix	brain
11	chr4:53510200-53523800	Weak transcription	NHLF	lung
12	chr4:53510400-53518400	Weak transcription	Fetal Muscle Leg	muscle
13	chr4:53510400-53523600	Weak transcription	Fetal Intestine Large	intestine
14	chr4:53510400-53523800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr4:53510400-53523800	Weak transcription	Fetal Stomach	stomach
16	chr4:53510400-53523800	Weak transcription	HSMM	muscle
17	chr4:53510600-53518200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr4:53510600-53518400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:53510600-53521000	Weak transcription	Brain Anterior Caudate	brain
20	chr4:53510600-53521200	Weak transcription	Fetal Lung	lung
21	chr4:53510600-53523600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:53510600-53523600	Weak transcription	Brain Angular Gyrus	brain
23	chr4:53510600-53523800	Weak transcription	NHDF-Ad	bronchial
24	chr4:53510800-53521800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:53510800-53522200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr4:53510800-53523600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:53510800-53523800	Weak transcription	Liver	Liver
28	chr4:53510800-53524400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr4:53511200-53523600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr4:53511600-53524600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr4:53512000-53524400	Weak transcription	Primary B cells from cord blood	blood
32	chr4:53513800-53524600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr4:53514200-53522400	Weak transcription	Ovary	ovary
34	chr4:53514200-53523800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr4:53514200-53524000	Weak transcription	HUVEC	blood vessel
36	chr4:53514400-53518200	Weak transcription	Right Ventricle	heart
37	chr4:53514400-53518200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr4:53514400-53522800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr4:53514600-53518200	Weak transcription	Brain Substantia Nigra	brain
40	chr4:53514600-53521400	Weak transcription	Aorta	Aorta
41	chr4:53514800-53518200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr4:53515400-53519200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:53515400-53521200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr4:53515600-53518200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr4:53515600-53522800	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr4:53515600-53524000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr4:53516200-53522400	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr4:53516400-53521000	Weak transcription	Fetal Heart	heart
49	chr4:53517200-53518200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:53517200-53518400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links