Variant report

Variant	rs2241621
Chromosome Location	chr14:81737076-81737077
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:81733049..81735838-chr14:81736167..81738052,2	MCF-7	breast:
2	chr14:81733496..81737456-chr14:81918664..81922273,4	MCF-7	breast:
3	chr14:81730236..81733765-chr14:81735324..81738162,3	K562	blood:
4	chr14:81736225..81738545-chr14:81918216..81919957,2	MCF-7	breast:
5	chr14:81684348..81690583-chr14:81729061..81738251,32	MCF-7	breast:
6	chr14:81683224..81690294-chr14:81730621..81737433,21	MCF-7	breast:
7	chr14:81684594..81689943-chr14:81730721..81738333,8	K562	blood:

Variant related genes	Relation type
ENSG00000165417	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10133562	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10149681	0.91[CHB][hapmap]
rs10483975	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11159494	0.85[CEU][hapmap]
rs11621116	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs11622105	0.81[EUR][1000 genomes]
rs11625861	0.84[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.96[MEX][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12147118	0.81[CHB][hapmap]
rs1864167	0.87[MEX][hapmap]
rs1885601	0.81[CEU][hapmap];0.87[MEX][hapmap]
rs1951614	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs1957546	0.87[CHB][hapmap]
rs1991516	0.85[CEU][hapmap]
rs2241622	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2288499	0.88[CEU][hapmap];0.83[MEX][hapmap]
rs2371570	0.86[EUR][1000 genomes]
rs2371571	0.82[EUR][1000 genomes]
rs3815953	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs55742437	0.82[EUR][1000 genomes]
rs61978870	0.82[EUR][1000 genomes]
rs6574631	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs6574634	0.93[ASN][1000 genomes]
rs7141288	0.82[EUR][1000 genomes]
rs7149103	0.86[ASN][1000 genomes]
rs7149294	0.88[ASN][1000 genomes]
rs7149672	0.82[CHB][hapmap]
rs7160342	0.83[EUR][1000 genomes]
rs7160569	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7160599	0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7161073	0.86[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs72695758	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs759939	0.85[CEU][hapmap]
rs8007595	0.94[ASN][1000 genomes]
rs8007841	0.91[CHB][hapmap]
rs8008870	0.85[EUR][1000 genomes]
rs8009696	0.84[ASN][1000 genomes]
rs8009888	0.91[ASN][1000 genomes]
rs8015423	1.00[CEU][hapmap];0.82[CHD][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes]
rs8016982	0.82[CHB][hapmap]
rs8019108	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs9646167	0.81[CEU][hapmap]
rs9806020	0.87[CHB][hapmap]
rs9806027	0.91[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs9944085	0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.88[MEX][hapmap];0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832841	chr14:81588322-81743921	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	86 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2241621	STON2	cis	brain	BrainEAC
rs2241621	STON2	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:81714200-81738600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr14:81721200-81742400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr14:81721400-81739800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr14:81721600-81739800	Weak transcription	Ovary	ovary
5	chr14:81722600-81741800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr14:81724600-81741800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr14:81724600-81746000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr14:81725000-81739800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr14:81725000-81740000	Weak transcription	Esophagus	oesophagus
10	chr14:81725000-81743600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr14:81727800-81746200	Weak transcription	NHDF-Ad	bronchial
12	chr14:81729400-81752600	Weak transcription	Stomach Mucosa	stomach
13	chr14:81730600-81743000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr14:81730600-81744000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr14:81730800-81740000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr14:81730800-81743600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr14:81731600-81739200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr14:81732400-81743600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr14:81733200-81753000	Weak transcription	Hela-S3	cervix
20	chr14:81734600-81737200	Weak transcription	Colonic Mucosa	Colon
21	chr14:81734600-81741400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr14:81734600-81742400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr14:81734800-81738800	Weak transcription	HSMMtube	muscle
24	chr14:81734800-81743000	Weak transcription	Placenta	Placenta
25	chr14:81734800-81743400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr14:81734800-81744000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr14:81735000-81739200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr14:81735000-81739600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr14:81735000-81739600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr14:81735200-81738400	Strong transcription	NHEK	skin
31	chr14:81735400-81737200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr14:81735400-81737200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr14:81735400-81739600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr14:81735600-81737600	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr14:81735600-81737600	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr14:81735600-81738000	Enhancers	Brain Anterior Caudate	brain
37	chr14:81735600-81739000	Weak transcription	HMEC	breast
38	chr14:81735600-81760200	Weak transcription	Primary hematopoietic stem cells	blood
39	chr14:81735800-81743000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr14:81735800-81746400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr14:81736000-81737200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr14:81736000-81741800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr14:81736000-81743400	Weak transcription	Fetal Intestine Large	intestine
44	chr14:81736000-81746000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr14:81736200-81742000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr14:81736400-81737600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr14:81736400-81737600	Enhancers	Spleen	Spleen
48	chr14:81736400-81737800	Genic enhancers	Fetal Muscle Leg	muscle
49	chr14:81736400-81738000	Strong transcription	Fetal Intestine Small	intestine
50	chr14:81736400-81738800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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