Variant report

Variant	rs28637676
Chromosome Location	chr12:122013041-122013042
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122007608..122010273-chr12:122010916..122013291,2	K562	blood:
2	chr12:122009958..122015218-chr12:122015373..122021843,8	K562	blood:
3	chr12:122005636..122007541-chr12:122010877..122013772,3	K562	blood:
4	chr12:122011717..122015728-chr12:122062639..122068006,6	MCF-7	breast:
5	chr12:121997898..122000701-chr12:122012949..122016939,4	MCF-7	breast:
6	chr12:122011020..122013695-chr12:122061585..122064129,2	K562	blood:
7	chr12:122011808..122013915-chr12:122017353..122019208,2	MCF-7	breast:
8	chr12:122011245..122016704-chr12:122016774..122020216,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000089094	Chromatin interaction
ENSG00000256742	Chromatin interaction
ENSG00000182500	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10840648	0.91[CEU][hapmap]
rs11043316	0.91[CEU][hapmap]
rs28378998	0.88[YRI][hapmap]
rs28421662	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7484839	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28637676	ARL6IP4	cis	parietal	SCAN
rs28637676	KCNC2	trans	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121976600-122014600	Weak transcription	Colonic Mucosa	Colon
2	chr12:121977200-122015200	Weak transcription	Small Intestine	intestine
3	chr12:121987600-122016800	Weak transcription	Aorta	Aorta
4	chr12:121990600-122013600	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr12:121996200-122015400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr12:121999400-122014200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:122001200-122013400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:122003200-122013800	Weak transcription	Esophagus	oesophagus
9	chr12:122004200-122013400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:122005200-122014400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:122006200-122014600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:122006400-122013800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr12:122006600-122013200	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr12:122006600-122014800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr12:122007000-122013800	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr12:122007000-122014600	Weak transcription	Fetal Kidney	kidney
17	chr12:122007200-122013600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:122007400-122013800	Weak transcription	Fetal Brain Male	brain
19	chr12:122007400-122014400	Weak transcription	GM12878-XiMat	blood
20	chr12:122007600-122014400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:122007600-122014600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr12:122007600-122014600	Weak transcription	A549	lung
23	chr12:122007600-122014600	Weak transcription	HSMM	muscle
24	chr12:122007800-122013200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:122008000-122013600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:122008000-122014600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:122008000-122016000	Weak transcription	Right Atrium	heart
28	chr12:122008200-122013200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:122008200-122013200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:122008200-122013400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:122008200-122014000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:122008200-122014000	Strong transcription	Fetal Thymus	thymus
33	chr12:122008200-122014800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr12:122008400-122013200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:122008400-122013800	Strong transcription	Fetal Stomach	stomach
36	chr12:122008600-122013800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:122008800-122014200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr12:122009200-122013800	Weak transcription	NH-A	brain
39	chr12:122009200-122014200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:122009600-122013400	Weak transcription	Fetal Brain Female	brain
41	chr12:122009600-122014800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:122009800-122013200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:122010200-122014000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:122010800-122015200	Weak transcription	Primary B cells from cord blood	blood
45	chr12:122011200-122014000	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr12:122011200-122016200	Weak transcription	HUVEC	blood vessel
47	chr12:122011400-122013800	Strong transcription	Adipose Nuclei	Adipose
48	chr12:122011600-122013600	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr12:122011600-122014200	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr12:122011600-122014200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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