Variant report

Variant	rs12616455
Chromosome Location	chr2:85696551-85696552
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85635544..85709381-chr2:85757395..85791508,633	K562	blood:
2	chr2:85695182..85700475-chr2:85771258..85775492,7	K562	blood:
3	chr2:85621158..85625123-chr2:85696021..85698114,3	MCF-7	breast:
4	chr2:85685085..85687339-chr2:85695524..85698451,3	K562	blood:
5	chr2:85693140..85697002-chr2:85763876..85768390,8	K562	blood:
6	chr2:85695571..85701406-chr2:85763524..85768199,9	MCF-7	breast:
7	chr2:85685085..85687339-chr2:85695524..85697541,2	K562	blood:
8	chr2:85696007..85697729-chr2:85764529..85767236,2	MCF-7	breast:
9	chr2:85688025..85690495-chr2:85693950..85697263,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000115486	Chromatin interaction
ENSG00000266577	Chromatin interaction
ENSG00000168906	Chromatin interaction
ENSG00000118640	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12714141	0.87[ASN][1000 genomes]
rs35700171	1.00[JPT][hapmap]
rs7577642	0.80[CEU][hapmap];0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005351	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv535803	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
3	nsv834283	chr2:85609500-85755708	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12616455	REEP1	cis	parietal	SCAN
rs12616455	RNF103	cis	parietal	SCAN
rs12616455	GGCX	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85693400-85701400	Enhancers	Fetal Intestine Small	intestine
2	chr2:85694200-85696800	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr2:85694400-85696800	Enhancers	Duodenum Mucosa	Duodenum
4	chr2:85694400-85700600	Enhancers	Fetal Intestine Large	intestine
5	chr2:85694800-85696600	Enhancers	Stomach Mucosa	stomach
6	chr2:85695000-85697200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:85695000-85697400	Enhancers	Pancreas	Pancrea
8	chr2:85695200-85696600	Flanking Active TSS	HepG2	liver
9	chr2:85695200-85697800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:85695200-85700800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:85695400-85698000	Weak transcription	Colonic Mucosa	Colon
12	chr2:85695600-85697800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:85695600-85697800	Weak transcription	Small Intestine	intestine
14	chr2:85695800-85697800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:85696000-85697200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:85696000-85698000	Weak transcription	HSMM	muscle
17	chr2:85696000-85698800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:85696000-85699400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:85696200-85696800	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr2:85696200-85697200	Enhancers	Hela-S3	cervix
21	chr2:85696200-85697600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:85696200-85697600	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:85696200-85698000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:85696200-85698000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:85696200-85698000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr2:85696200-85698400	Weak transcription	Colon Smooth Muscle	Colon
27	chr2:85696200-85698400	Weak transcription	Fetal Stomach	stomach
28	chr2:85696200-85698400	Enhancers	A549	lung
29	chr2:85696200-85698400	Weak transcription	NHDF-Ad	bronchial
30	chr2:85696200-85698600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr2:85696200-85698600	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:85696200-85698800	Weak transcription	Brain Anterior Caudate	brain
33	chr2:85696200-85699200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr2:85696200-85699600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:85696200-85699600	Enhancers	Liver	Liver
36	chr2:85696200-85699800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr2:85696200-85703200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:85696400-85696600	Enhancers	K562	blood
39	chr2:85696400-85696800	Weak transcription	HSMMtube	muscle
40	chr2:85696400-85697400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr2:85696400-85697600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr2:85696400-85697600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:85696400-85697600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:85696400-85697600	Weak transcription	Placenta	Placenta
45	chr2:85696400-85697800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:85696400-85697800	Weak transcription	HMEC	breast
47	chr2:85696400-85697800	Weak transcription	NHEK	skin
48	chr2:85696400-85698000	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr2:85696400-85698000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:85696400-85698000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links