Variant report

Variant	rs253484
Chromosome Location	chr5:16898070-16898071
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:16895872..16898424-chr5:16934812..16936470,2	MCF-7	breast:
2	chr5:16892933..16897070-chr5:16897498..16901971,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145555	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs16869222	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs16869226	0.90[YRI][hapmap];0.85[AFR][1000 genomes]
rs253483	0.92[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs253485	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2560842	0.93[CEU][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2560843	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2560844	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2560846	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2560848	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2560850	0.80[CHB][hapmap]
rs2562350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562352	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2562353	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2562354	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2562356	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2562357	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2562358	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2625172	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2625173	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2625174	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2625175	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56997603	0.85[AFR][1000 genomes]
rs60434528	0.85[AFR][1000 genomes]
rs62371016	0.85[AMR][1000 genomes]
rs6896099	0.97[YRI][hapmap];0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv2762500	chr5:16815489-16952565	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv1034844	chr5:16854341-16903100	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3485757	chr5:16856475-16966851	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	esv3485758	chr5:16856475-16966851	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16893400-16898400	Enhancers	Fetal Intestine Large	intestine
2	chr5:16893600-16898400	Enhancers	Colonic Mucosa	Colon
3	chr5:16893600-16899000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:16893800-16898200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:16893800-16898200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:16893800-16898200	Enhancers	Pancreas	Pancrea
7	chr5:16893800-16898600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:16894000-16898200	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr5:16894000-16898200	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr5:16894000-16898400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:16894000-16898400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:16894000-16898400	Enhancers	HUVEC	blood vessel
13	chr5:16894000-16899000	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr5:16894200-16898200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:16894200-16898200	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr5:16894200-16898200	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr5:16894200-16898200	Enhancers	Placenta	Placenta
18	chr5:16894200-16898400	Enhancers	H1 Cell Line	embryonic stem cell
19	chr5:16894200-16898400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:16894200-16898400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr5:16894200-16898400	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr5:16894200-16898400	Enhancers	Fetal Muscle Leg	muscle
23	chr5:16894200-16898800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr5:16894400-16898200	Enhancers	Gastric	stomach
25	chr5:16894400-16898400	Enhancers	Fetal Lung	lung
26	chr5:16894400-16900000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:16894600-16898400	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr5:16894600-16898600	Enhancers	NHEK	skin
29	chr5:16894800-16898200	Enhancers	Psoas Muscle	Psoas
30	chr5:16894800-16898400	Enhancers	H9 Cell Line	embryonic stem cell
31	chr5:16894800-16898400	Enhancers	Fetal Stomach	stomach
32	chr5:16894800-16898400	Enhancers	Lung	lung
33	chr5:16894800-16898400	Enhancers	Ovary	ovary
34	chr5:16895000-16898200	Enhancers	Osteobl	bone
35	chr5:16895000-16898400	Enhancers	Duodenum Mucosa	Duodenum
36	chr5:16895000-16903000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr5:16895200-16898200	Enhancers	Stomach Mucosa	stomach
38	chr5:16895600-16898200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:16895600-16898400	Enhancers	Small Intestine	intestine
40	chr5:16895600-16902000	Enhancers	Hela-S3	cervix
41	chr5:16895800-16898400	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr5:16896000-16901200	Weak transcription	Spleen	Spleen
43	chr5:16896000-16912400	Weak transcription	Esophagus	oesophagus
44	chr5:16896400-16901200	Weak transcription	Left Ventricle	heart
45	chr5:16896600-16898200	Enhancers	NHLF	lung
46	chr5:16896800-16898400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr5:16897000-16898200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:16897000-16898200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:16897000-16898200	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr5:16897000-16898200	Enhancers	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links