Variant report

Variant	rs4898541
Chromosome Location	chr12:50262172-50262173
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50261492..50264871-chr12:50267070..50272951,8	MCF-7	breast:
2	chr12:50257760..50259370-chr12:50261533..50263034,2	MCF-7	breast:
3	chr12:50261163..50264047-chr12:50337700..50340324,2	MCF-7	breast:
4	chr12:50259914..50262482-chr12:50360681..50362364,3	K562	blood:
5	chr12:50256208..50258929-chr12:50261762..50264247,4	K562	blood:
6	chr12:50259734..50262522-chr12:50450953..50452874,2	MCF-7	breast:
7	chr12:50261251..50262807-chr12:50275153..50277323,2	MCF-7	breast:
8	chr12:50236290..50238561-chr12:50261211..50262795,2	K562	blood:
9	chr12:50260529..50262269-chr12:50360474..50361834,19	MCF-7	breast:
10	chr12:50260980..50264141-chr12:50355537..50358895,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000086159	Chromatin interaction
ENSG00000110881	Chromatin interaction
ENSG00000161798	Chromatin interaction
ENSG00000186666	Chromatin interaction
ENSG00000242041	Chromatin interaction
ENSG00000257588	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1454193	1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4898538	0.93[CEU][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap]
rs7953118	0.93[CEU][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv832407	chr12:50243268-50412236	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4898541	C12orf62	cis	parietal	SCAN
rs4898541	ELP3	trans	cerebellum	SCAN
rs4898541	PFKM	cis	parietal	SCAN
rs4898541	TMEM106C	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50260600-50262600	Enhancers	K562	blood
2	chr12:50260600-50262800	Enhancers	Fetal Muscle Trunk	muscle
3	chr12:50260600-50263000	Flanking Active TSS	Hela-S3	cervix
4	chr12:50260600-50263200	Enhancers	Fetal Brain Female	brain
5	chr12:50260600-50263400	Enhancers	Brain Anterior Caudate	brain
6	chr12:50260600-50263800	Enhancers	Brain Hippocampus Middle	brain
7	chr12:50260600-50264600	Enhancers	Fetal Brain Male	brain
8	chr12:50260600-50265200	Enhancers	Right Ventricle	heart
9	chr12:50260600-50267600	Enhancers	HSMM	muscle
10	chr12:50260600-50268200	Enhancers	HSMMtube	muscle
11	chr12:50260600-50268600	Enhancers	Fetal Muscle Leg	muscle
12	chr12:50260800-50262200	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr12:50260800-50263400	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr12:50260800-50263600	Enhancers	Brain Angular Gyrus	brain
15	chr12:50260800-50263600	Enhancers	Brain Cingulate Gyrus	brain
16	chr12:50260800-50263600	Enhancers	Brain Substantia Nigra	brain
17	chr12:50260800-50263800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:50260800-50263800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:50260800-50263800	Enhancers	Pancreas	Pancrea
20	chr12:50260800-50263800	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr12:50260800-50263800	Enhancers	Stomach Mucosa	stomach
22	chr12:50260800-50264000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:50260800-50264000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr12:50260800-50264000	Enhancers	Fetal Intestine Small	intestine
25	chr12:50261000-50262200	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr12:50261000-50262600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:50261000-50262600	Bivalent Enhancer	NHLF	lung
28	chr12:50261000-50263400	Enhancers	Brain Germinal Matrix	brain
29	chr12:50261000-50263400	Enhancers	Duodenum Mucosa	Duodenum
30	chr12:50261000-50263600	Enhancers	Fetal Stomach	stomach
31	chr12:50261000-50263800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
32	chr12:50261000-50264200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:50261000-50264200	Enhancers	Fetal Lung	lung
34	chr12:50261000-50264200	Enhancers	Placenta	Placenta
35	chr12:50261000-50265000	Enhancers	Fetal Heart	heart
36	chr12:50261000-50265400	Enhancers	Placenta Amnion	Placenta Amnion
37	chr12:50261000-50268200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:50261200-50262400	Enhancers	Spleen	Spleen
39	chr12:50261200-50262600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:50261200-50262600	Enhancers	Colon Smooth Muscle	Colon
41	chr12:50261200-50262800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:50261200-50263800	Enhancers	Colonic Mucosa	Colon
43	chr12:50261200-50263800	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr12:50261200-50263800	Enhancers	Fetal Intestine Large	intestine
45	chr12:50261200-50263800	Enhancers	Lung	lung
46	chr12:50261200-50264000	Enhancers	Stomach Smooth Muscle	stomach
47	chr12:50261200-50264600	Enhancers	Left Ventricle	heart
48	chr12:50261200-50265000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:50261200-50267000	Enhancers	Right Atrium	heart
50	chr12:50261400-50263200	Enhancers	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links