Variant report

Variant	rs12127819
Chromosome Location	chr1:227952758-227952759
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227946182..227953403-chr1:228132950..228136592,12	MCF-7	breast:
2	chr1:227951444..227953989-chr1:228132939..228135911,4	MCF-7	breast:
3	chr1:227951099..227952899-chr1:227953091..227955822,2	K562	blood:
4	chr1:227913567..227919162-chr1:227947935..227954215,6	MCF-7	breast:
5	chr1:227952215..227955097-chr1:227966264..227970414,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143740	Chromatin interaction
ENSG00000143816	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10799445	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10916204	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12073225	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12077397	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12097239	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12141801	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3088389	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6664307	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv468238	chr1:227935762-228045748	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv549272	chr1:227935762-228045748	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12127819	JMJD4	cis	multi-tissue	Pritchard
rs12127819	ZNF678	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227924200-227955000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:227945800-227954800	Weak transcription	Fetal Kidney	kidney
3	chr1:227946000-227960400	Strong transcription	Fetal Brain Female	brain
4	chr1:227947600-227954800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:227947800-227955400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:227948000-227953600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:227948200-227954600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:227948400-227955400	Weak transcription	Psoas Muscle	Psoas
9	chr1:227948400-227956000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr1:227948600-227955600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr1:227948800-227952800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:227949000-227953400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:227949200-227954400	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr1:227949200-227954800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:227949200-227956000	Genic enhancers	Fetal Thymus	thymus
16	chr1:227949400-227954200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:227949400-227954400	Enhancers	Placenta Amnion	Placenta Amnion
18	chr1:227949400-227954600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:227949600-227952800	Enhancers	HMEC	breast
20	chr1:227949600-227953400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr1:227949600-227954400	Weak transcription	Brain Substantia Nigra	brain
22	chr1:227949600-227955400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:227949600-227955600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:227949800-227954600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:227950000-227953000	Enhancers	NHEK	skin
26	chr1:227950000-227953600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:227950000-227954000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:227950000-227954200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:227950000-227954600	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr1:227950200-227952800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:227950200-227953600	Enhancers	Primary T cells fromperipheralblood	blood
32	chr1:227950200-227954600	Weak transcription	HepG2	liver
33	chr1:227950200-227955000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:227950200-227955200	Weak transcription	Ovary	ovary
35	chr1:227950400-227953200	Genic enhancers	NHLF	lung
36	chr1:227950600-227952800	Weak transcription	GM12878-XiMat	blood
37	chr1:227950600-227953200	Weak transcription	Stomach Mucosa	stomach
38	chr1:227950600-227953400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:227950600-227953400	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr1:227950600-227953400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:227950600-227953600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:227950600-227953600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:227950600-227953600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr1:227950600-227954000	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr1:227950600-227954200	Enhancers	Primary T cells from cord blood	blood
46	chr1:227950600-227954600	Weak transcription	Primary B cells from cord blood	blood
47	chr1:227950600-227954600	Weak transcription	Fetal Brain Male	brain
48	chr1:227950800-227953200	Strong transcription	Fetal Intestine Large	intestine
49	chr1:227950800-227953800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr1:227950800-227953800	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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