Variant report

Variant	rs25644
Chromosome Location	chr12:121666646-121666647
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:121666090..121669827-chr12:121670263..121674205,6	K562	blood:
2	chr12:121664342..121666780-chr12:121734216..121737104,3	MCF-7	breast:
3	chr12:121565146..121566829-chr12:121666395..121668307,2	MCF-7	breast:
4	chr12:121654852..121658533-chr12:121664523..121668061,3	K562	blood:
5	chr12:121646834..121652613-chr12:121661734..121667006,9	MCF-7	breast:
6	chr12:121662095..121663648-chr12:121665319..121667911,2	K562	blood:
7	chr12:121664133..121666878-chr12:121668504..121670264,2	K562	blood:
8	chr12:121661635..121663978-chr12:121665688..121668181,3	MCF-7	breast:
9	chr12:121521823..121524170-chr12:121665223..121666931,2	MCF-7	breast:
10	chr12:121666081..121668034-chr12:121878369..121881222,2	MCF-7	breast:
11	chr12:121657033..121659452-chr12:121666561..121668360,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000089094	Chromatin interaction
ENSG00000110931	Chromatin interaction
ENSG00000135124	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10774588	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10849852	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10849859	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849861	1.00[CEU][hapmap];0.80[CHB][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10849862	0.84[EUR][1000 genomes]
rs11065479	0.84[ASN][1000 genomes]
rs11065483	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11065508	0.84[EUR][1000 genomes]
rs1132780	1.00[CEU][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs1151880	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1169717	0.93[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1169718	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12298365	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12304301	0.84[EUR][1000 genomes]
rs1560568	1.00[CEU][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs2393849	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs2393850	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2668250	0.84[EUR][1000 genomes]
rs2686362	0.80[CHB][hapmap];0.84[ASN][1000 genomes]
rs28360463	0.88[ASN][1000 genomes]
rs3794203	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3794208	1.00[CEU][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3794209	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3815989	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4980998	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58232824	0.91[AMR][1000 genomes]
rs59304889	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61216528	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132846	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs7298368	1.00[LWK][hapmap];0.95[MEX][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes]
rs7975295	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7975910	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1054878	chr12:121519880-121761800	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv455729	chr12:121525591-121761800	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv560455	chr12:121525591-121761800	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1050519	chr12:121552964-121756420	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer 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	22 gene(s)	inside rSNPs	diseases
7	nsv899564	chr12:121641509-121689798	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv899565	chr12:121641509-121698785	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121649000-121675800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr12:121649000-121676200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:121649000-121676200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr12:121649000-121676600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr12:121649400-121680200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:121652400-121675600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr12:121653200-121675600	Weak transcription	HSMMtube	muscle
8	chr12:121653200-121698800	Weak transcription	Fetal Heart	heart
9	chr12:121653400-121673600	Weak transcription	Osteobl	bone
10	chr12:121653400-121677600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr12:121653400-121678600	Weak transcription	Right Atrium	heart
12	chr12:121653600-121670200	Weak transcription	NHDF-Ad	bronchial
13	chr12:121654800-121675200	Strong transcription	Fetal Stomach	stomach
14	chr12:121655200-121678000	Weak transcription	Fetal Kidney	kidney
15	chr12:121655400-121667400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:121655400-121667800	Weak transcription	A549	lung
17	chr12:121657000-121671600	Weak transcription	HUVEC	blood vessel
18	chr12:121657000-121676200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr12:121658200-121673600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:121658800-121671600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr12:121659400-121667600	Strong transcription	Fetal Muscle Leg	muscle
22	chr12:121660800-121667600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr12:121661600-121667600	Weak transcription	Hela-S3	cervix
24	chr12:121661600-121667800	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr12:121661600-121675800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr12:121661600-121675800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr12:121661800-121671000	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr12:121662000-121666800	Weak transcription	Brain Germinal Matrix	brain
29	chr12:121662000-121671000	Weak transcription	Aorta	Aorta
30	chr12:121662000-121673000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:121662000-121673600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:121662000-121676800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr12:121662000-121679000	Weak transcription	K562	blood
34	chr12:121662400-121676400	Weak transcription	Primary B cells from cord blood	blood
35	chr12:121662600-121673800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:121662800-121690600	Weak transcription	Fetal Brain Male	brain
37	chr12:121663200-121675800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr12:121663600-121666800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:121663600-121667600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:121663600-121668000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr12:121663600-121675800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:121663800-121668000	Strong transcription	Fetal Muscle Trunk	muscle
43	chr12:121664000-121676200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:121664400-121668600	Genic enhancers	Fetal Intestine Small	intestine
45	chr12:121664400-121672400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:121664400-121673600	Weak transcription	Fetal Lung	lung
47	chr12:121665000-121667800	Strong transcription	Brain Cingulate Gyrus	brain
48	chr12:121665400-121668200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr12:121665400-121670800	Weak transcription	Small Intestine	intestine
50	chr12:121665600-121668400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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