Variant report

Variant	rs12025942
Chromosome Location	chr1:227758505-227758506
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227753749..227755890-chr1:227756873..227759865,3	K562	blood:
2	chr1:227758119..227760802-chr16:33923322..33925835,2	MCF-7	breast:
3	chr1:227747468..227754046-chr1:227756230..227762193,11	K562	blood:
4	chr1:227751815..227753395-chr1:227758245..227760827,2	K562	blood:

Variant related genes	Relation type
ENSG00000181450	Chromatin interaction
ENSG00000202264	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1056699	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1060295	0.92[CEU][hapmap]
rs10799430	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10799439	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916171	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10916188	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916191	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916203	0.85[CEU][hapmap]
rs1155807	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12033000	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12033610	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1810680	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1923823	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2104245	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2132368	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2172937	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2236360	0.92[CEU][hapmap]
rs4500311	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4653856	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6426468	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6426473	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6660432	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6693054	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6703846	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs730684	0.85[CEU][hapmap]
rs7526184	0.92[CEU][hapmap]
rs7533588	0.88[CEU][hapmap]
rs7534403	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7536765	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7539282	0.92[CEU][hapmap]

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	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv2753828	chr1:227670265-227791265	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv873248	chr1:227710381-227786033	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3338615	chr1:227738421-227798486	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3327012	chr1:227741102-227890968	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv947073	chr1:227755113-227760558	ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12025942	ZNF678	cis	normal skin	skin_eQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227752000-227759800	Weak transcription	Left Ventricle	heart
2	chr1:227752000-227760000	Weak transcription	Esophagus	oesophagus
3	chr1:227752000-227766800	Weak transcription	Ovary	ovary
4	chr1:227752200-227758800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:227752200-227760000	Weak transcription	Fetal Intestine Large	intestine
6	chr1:227752200-227763200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:227752200-227774400	Weak transcription	Aorta	Aorta
8	chr1:227752400-227759600	Weak transcription	Primary T cells from cord blood	blood
9	chr1:227752400-227759800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:227752400-227759800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:227752400-227759800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:227752400-227760000	Weak transcription	Fetal Kidney	kidney
13	chr1:227752400-227760000	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:227752400-227760000	Weak transcription	NHEK	skin
15	chr1:227752400-227760200	Weak transcription	Fetal Heart	heart
16	chr1:227752400-227760200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:227752400-227763000	Weak transcription	Stomach Mucosa	stomach
18	chr1:227752400-227763800	Weak transcription	HSMMtube	muscle
19	chr1:227752400-227766800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:227752400-227780600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:227752600-227759800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr1:227752600-227760000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr1:227752600-227760000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:227752600-227760000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:227752800-227759400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:227753200-227760000	Weak transcription	Small Intestine	intestine
27	chr1:227753600-227763000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:227754000-227759800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:227754200-227760000	Weak transcription	Thymus	Thymus
30	chr1:227754400-227759800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:227754400-227760000	Weak transcription	Fetal Stomach	stomach
32	chr1:227754400-227783600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:227755800-227760000	Weak transcription	HSMM	muscle
34	chr1:227756800-227759800	Weak transcription	K562	blood
35	chr1:227756800-227760000	Weak transcription	Right Ventricle	heart
36	chr1:227756800-227760000	Weak transcription	Spleen	Spleen
37	chr1:227756800-227760200	Weak transcription	Psoas Muscle	Psoas
38	chr1:227756800-227760400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr1:227756800-227762400	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr1:227757000-227760000	Weak transcription	Gastric	stomach
41	chr1:227757600-227758600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:227758000-227760000	Weak transcription	Pancreas	Pancrea
43	chr1:227758200-227759800	Weak transcription	Fetal Lung	lung
44	chr1:227758400-227759400	Weak transcription	Osteobl	bone
45	chr1:227758400-227760000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:227758400-227761400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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