Variant report

Variant	rs28564254
Chromosome Location	chr16:75289609-75289610
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:75288407-75289624	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr16:75289291-75289894	HepG2	liver:	n/a	n/a
3	POLR2A	chr16:75288200-75289630	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:75288495..75290514-chr16:75396856..75398580,2	MCF-7	breast:
2	chr16:75261304..75263525-chr16:75287372..75289617,2	K562	blood:
3	chr16:75288586..75292639-chr16:75337750..75340619,6	MCF-7	breast:

Variant related genes	Relation type
BCAR1	TF binding region
ENSG00000153774	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2278020	0.88[ASN][1000 genomes]
rs36097424	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3743613	0.92[ASN][1000 genomes]
rs4887810	0.85[ASN][1000 genomes]
rs57613349	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8046743	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
3	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
4	nsv1056082	chr16:75004990-75295847	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv833282	chr16:75154171-75330634	Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv516504	chr16:75223491-75306402	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv523405	chr16:75227969-75342846	Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	esv1806781	chr16:75235390-75307470	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv906909	chr16:75236154-75316074	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	esv1792587	chr16:75237936-75305783	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv906910	chr16:75251299-75316074	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv906911	chr16:75252526-75296247	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv906912	chr16:75252526-75320827	Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	esv1813349	chr16:75257361-75302684	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
15	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
16	nsv906913	chr16:75267743-75306402	Genic enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
17	nsv471095	chr16:75269533-75320827	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
18	esv1843498	chr16:75271642-75296844	Genic enhancers Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75285600-75291600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:75285600-75292400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr16:75285600-75293000	Enhancers	Lung	lung
4	chr16:75285600-75293000	Enhancers	Placenta Amnion	Placenta Amnion
5	chr16:75285600-75293200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr16:75285800-75292800	Enhancers	Right Atrium	heart
7	chr16:75286000-75290400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr16:75286000-75290600	Enhancers	Right Ventricle	heart
9	chr16:75286000-75292000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr16:75286000-75292000	Enhancers	Esophagus	oesophagus
11	chr16:75286000-75292200	Enhancers	Stomach Mucosa	stomach
12	chr16:75286000-75292200	Enhancers	NHEK	skin
13	chr16:75286000-75292400	Enhancers	Fetal Intestine Large	intestine
14	chr16:75286000-75293000	Enhancers	Left Ventricle	heart
15	chr16:75286000-75293000	Enhancers	Ovary	ovary
16	chr16:75286000-75293200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr16:75286000-75293200	Enhancers	Fetal Lung	lung
18	chr16:75286000-75293200	Enhancers	NHDF-Ad	bronchial
19	chr16:75286000-75293400	Enhancers	HMEC	breast
20	chr16:75286000-75297400	Enhancers	Psoas Muscle	Psoas
21	chr16:75286000-75297600	Genic enhancers	Fetal Intestine Small	intestine
22	chr16:75286000-75298000	Genic enhancers	Fetal Stomach	stomach
23	chr16:75286200-75289800	Weak transcription	K562	blood
24	chr16:75286200-75290400	Enhancers	HSMMtube	muscle
25	chr16:75286200-75290800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr16:75286200-75291000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr16:75286200-75292200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr16:75286200-75293000	Enhancers	Brain Substantia Nigra	brain
29	chr16:75286200-75293200	Enhancers	H1 Cell Line	embryonic stem cell
30	chr16:75286200-75293200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr16:75286200-75293200	Enhancers	Fetal Heart	heart
32	chr16:75286200-75293400	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr16:75286400-75290000	Enhancers	Rectal Smooth Muscle	rectum
34	chr16:75286400-75290400	Weak transcription	Fetal Brain Male	brain
35	chr16:75286400-75290800	Enhancers	Brain Cingulate Gyrus	brain
36	chr16:75286400-75291200	Enhancers	Fetal Muscle Leg	muscle
37	chr16:75286400-75293000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr16:75286400-75293200	Enhancers	Brain Anterior Caudate	brain
39	chr16:75286600-75290400	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr16:75286600-75293400	Enhancers	Spleen	Spleen
41	chr16:75286800-75290000	Weak transcription	Small Intestine	intestine
42	chr16:75287200-75290400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr16:75287200-75290600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr16:75287400-75291600	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr16:75287600-75293200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr16:75287800-75290000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr16:75287800-75290000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr16:75287800-75290200	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr16:75287800-75291000	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr16:75287800-75291000	Enhancers	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links