Variant report

Variant	rs16969577
Chromosome Location	chr15:78504425-78504426
allele	C/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	MYC	chr15:78504422-78505408	NB4	blood:	n/a	chr15:78505144-78505153
2	MAZ	chr15:78504387-78505422	IMR90	lung:	n/a	chr15:78505144-78505153
3	SMARCC1	chr15:78504393-78505969	Hela-S3	cervix:	n/a	chr15:78505087-78505096
4	KAP1	chr15:78503711-78505453	U2OS	brain:	n/a	chr15:78505145-78505154 chr15:78504596-78504604 chr15:78505088-78505097

No.	Distal block	Cell Line	Cell type
1	chr15:78503669..78505180-chr5:127074238..127077145,2	MCF-7	breast:
2	chr15:78368511..78371047-chr15:78502666..78504614,2	MCF-7	breast:
3	chr15:78504380..78505262-chr15:78533049..78533611,2	MCF-7	breast:

Variant related genes	Relation type
ACSBG1	TF binding region
ENSG00000230561	Chromatin interaction
ENSG00000167202	Chromatin interaction
ENSG00000183476	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs11854143	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS 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 miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv948437	chr15:78435527-78504662	Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv904430	chr15:78466127-78507316	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78494200-78508800	Enhancers	Brain Inferior Temporal Lobe	brain
2	chr15:78494200-78509800	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr15:78494800-78508800	Enhancers	Brain Hippocampus Middle	brain
4	chr15:78494800-78509800	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr15:78495400-78510000	Enhancers	Pancreas	Pancrea
6	chr15:78495400-78511000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr15:78496000-78507200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:78496400-78507800	Enhancers	Brain Anterior Caudate	brain
9	chr15:78497200-78506800	Enhancers	Placenta Amnion	Placenta Amnion
10	chr15:78499600-78504600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:78499600-78504800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:78500800-78506200	Enhancers	Brain Angular Gyrus	brain
13	chr15:78501200-78506200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr15:78501400-78506000	Enhancers	Stomach Mucosa	stomach
15	chr15:78501600-78506000	Enhancers	Duodenum Mucosa	Duodenum
16	chr15:78501600-78506600	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr15:78501800-78505800	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr15:78502000-78505000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:78502000-78506600	Enhancers	Colon Smooth Muscle	Colon
20	chr15:78502200-78505800	Enhancers	K562	blood
21	chr15:78502200-78506400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:78502600-78504800	Weak transcription	Left Ventricle	heart
23	chr15:78502600-78508800	Weak transcription	Gastric	stomach
24	chr15:78502800-78505600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:78502800-78508200	Weak transcription	Liver	Liver
26	chr15:78503000-78504600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr15:78503000-78504600	Weak transcription	HSMMtube	muscle
28	chr15:78503000-78504800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:78503200-78504600	Weak transcription	Fetal Heart	heart
30	chr15:78503200-78504600	Weak transcription	Psoas Muscle	Psoas
31	chr15:78503200-78506600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:78503400-78505000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr15:78503400-78505400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:78503600-78504800	Enhancers	A549	lung
35	chr15:78503600-78506200	Enhancers	Colonic Mucosa	Colon
36	chr15:78503800-78506400	Enhancers	Fetal Muscle Leg	muscle
37	chr15:78503800-78507800	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr15:78504000-78506400	Enhancers	Right Ventricle	heart
39	chr15:78504000-78506600	Enhancers	Esophagus	oesophagus
40	chr15:78504000-78510000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr15:78504200-78504600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:78504200-78504600	Genic enhancers	Brain Cingulate Gyrus	brain
43	chr15:78504200-78505200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr15:78504200-78505600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:78504200-78506000	Enhancers	Placenta	Placenta
46	chr15:78504200-78506800	Enhancers	Right Atrium	heart
47	chr15:78504200-78507600	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr15:78504400-78504600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:78504400-78504800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr15:78504400-78504800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links