Variant report

Variant	rs28850594
Chromosome Location	chr4:7970589-7970590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7965044..7967214-chr4:7970387..7972613,2	MCF-7	breast:
2	chr4:7938506..7945813-chr4:7968503..7977501,21	MCF-7	breast:
3	chr4:7941236..7944392-chr4:7970174..7972613,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196526	Chromatin interaction
ENSG00000228919	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10008860	0.86[EUR][1000 genomes]
rs11722433	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11726359	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11730568	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731931	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11733842	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55943378	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73214069	0.87[AMR][1000 genomes];0.85[EUR][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	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv829851	chr4:7958698-8049060	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
6	nsv469779	chr4:7965253-8177646	Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv482448	chr4:7965253-8177646	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv878579	chr4:7969594-8011696	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28850594	AFAP1	cis	Whole Blood	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7959400-7971600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:7963000-7971600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:7963200-7971600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr4:7963200-7971800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:7963400-7975400	Weak transcription	Aorta	Aorta
6	chr4:7964400-7971600	Enhancers	Primary T cells fromperipheralblood	blood
7	chr4:7964800-7971000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr4:7965600-7971200	Weak transcription	Brain Anterior Caudate	brain
9	chr4:7966000-7971600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:7967000-7987600	Weak transcription	Psoas Muscle	Psoas
11	chr4:7967200-7971000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr4:7967200-7971000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr4:7967800-7970600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr4:7967800-7970600	Enhancers	A549	lung
15	chr4:7967800-7971000	Weak transcription	Fetal Lung	lung
16	chr4:7968000-7971000	Weak transcription	Fetal Heart	heart
17	chr4:7968200-7972000	Enhancers	Fetal Intestine Large	intestine
18	chr4:7968600-7970600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:7968600-7972000	Enhancers	Spleen	Spleen
20	chr4:7968800-7970600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr4:7968800-7970600	Enhancers	Brain Cingulate Gyrus	brain
22	chr4:7969000-7970600	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr4:7969000-7971600	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr4:7969000-7972000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:7969000-7975600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
26	chr4:7969200-7970600	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr4:7969200-7971200	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr4:7969200-7971200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr4:7969200-7971600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:7969200-7972000	Enhancers	Stomach Mucosa	stomach
31	chr4:7969200-7972400	Enhancers	Colon Smooth Muscle	Colon
32	chr4:7969200-7973400	Enhancers	Right Ventricle	heart
33	chr4:7969200-7974400	Enhancers	Fetal Muscle Leg	muscle
34	chr4:7969200-7975600	Enhancers	Fetal Thymus	thymus
35	chr4:7969200-7975800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:7969400-7971000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr4:7969400-7971200	Enhancers	Osteobl	bone
38	chr4:7969400-7971600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:7969400-7971600	Enhancers	Hela-S3	cervix
40	chr4:7969400-7971800	Enhancers	Rectal Smooth Muscle	rectum
41	chr4:7969400-7972000	Enhancers	Placenta	Placenta
42	chr4:7969400-7972000	Enhancers	Fetal Stomach	stomach
43	chr4:7969400-7972400	Enhancers	Fetal Muscle Trunk	muscle
44	chr4:7969400-7972400	Enhancers	NHDF-Ad	bronchial
45	chr4:7969400-7972600	Enhancers	Left Ventricle	heart
46	chr4:7969400-7972800	Enhancers	Right Atrium	heart
47	chr4:7969400-7973200	Enhancers	NHLF	lung
48	chr4:7969400-7974800	Enhancers	Lung	lung
49	chr4:7969400-7975800	Enhancers	Stomach Smooth Muscle	stomach
50	chr4:7969400-7976000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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