Variant report

Variant	rs12043790
Chromosome Location	chr1:223962943-223962944
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223962795..223965332-chr1:223971942..223974529,2	MCF-7	breast:
2	chr1:223941213..223943613-chr1:223960905..223963587,2	K562	blood:
3	chr1:223962452..223964542-chr1:223969395..223972147,3	K562	blood:
4	chr1:223962467..223965258-chr1:224032898..224035582,2	MCF-7	breast:
5	chr1:223961408..223964143-chr1:223997434..223999357,2	K562	blood:
6	chr1:223961851..223963368-chr1:223992052..223994188,2	K562	blood:

Variant related genes	Relation type
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10159015	0.81[ASN][1000 genomes]
rs12022914	1.00[CHD][hapmap];0.95[ASN][1000 genomes]
rs12022920	0.95[ASN][1000 genomes]
rs12024059	0.95[ASN][1000 genomes]
rs12025911	0.81[ASN][1000 genomes]
rs12026548	1.00[ASN][1000 genomes]
rs12027762	0.81[ASN][1000 genomes]
rs12028843	0.95[ASN][1000 genomes]
rs12031859	0.95[ASN][1000 genomes]
rs12034120	0.93[ASN][1000 genomes]
rs12034645	0.87[CHD][hapmap]
rs12034914	0.93[ASN][1000 genomes]
rs12035506	0.83[ASN][1000 genomes]
rs12036390	0.83[ASN][1000 genomes]
rs12036717	0.93[ASN][1000 genomes]
rs12038665	0.95[ASN][1000 genomes]
rs12038706	0.93[ASN][1000 genomes]
rs12039721	0.93[ASN][1000 genomes]
rs12040996	0.93[ASN][1000 genomes]
rs12044358	1.00[ASN][1000 genomes]
rs12044652	0.93[ASN][1000 genomes]
rs12044659	0.93[ASN][1000 genomes]
rs12047342	0.93[ASN][1000 genomes]
rs12047952	0.81[ASN][1000 genomes]
rs12088254	0.85[ASN][1000 genomes]
rs1542507	0.95[ASN][1000 genomes]
rs16842259	1.00[CHD][hapmap];0.95[ASN][1000 genomes]
rs28370095	0.93[ASN][1000 genomes]
rs28370112	0.93[ASN][1000 genomes]
rs28370115	0.93[ASN][1000 genomes]
rs28370160	0.98[ASN][1000 genomes]
rs28370166	1.00[ASN][1000 genomes]
rs28370174	1.00[ASN][1000 genomes]
rs28370177	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs28370178	1.00[ASN][1000 genomes]
rs3754088	0.93[ASN][1000 genomes]
rs3767710	1.00[ASN][1000 genomes]
rs3767712	0.93[ASN][1000 genomes]
rs3767713	0.93[ASN][1000 genomes]
rs3820474	0.95[ASN][1000 genomes]
rs3820481	0.93[ASN][1000 genomes]
rs60681980	0.81[ASN][1000 genomes]
rs61437308	0.95[ASN][1000 genomes]
rs61824005	0.85[ASN][1000 genomes]
rs747811	1.00[ASN][1000 genomes]
rs7538151	0.93[ASN][1000 genomes]
rs7552702	0.81[ASN][1000 genomes]
rs9804140	1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs9970756	0.93[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	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223954800-223964000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:223956600-223963400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:223956600-223963600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:223956600-223963600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:223956600-223963800	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr1:223956600-223967000	Strong transcription	Lung	lung
7	chr1:223956600-223967200	Strong transcription	Colonic Mucosa	Colon
8	chr1:223956600-223968400	Strong transcription	Fetal Brain Female	brain
9	chr1:223956600-223969000	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:223956600-223969000	Strong transcription	Fetal Stomach	stomach
11	chr1:223956600-224004600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr1:223956600-224004600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr1:223956800-223963000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:223956800-223963200	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:223956800-223969000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:223956800-223969200	Strong transcription	Placenta	Placenta
17	chr1:223956800-223974200	Strong transcription	Primary T cells from cord blood	blood
18	chr1:223956800-223974200	Strong transcription	Liver	Liver
19	chr1:223957000-223964000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr1:223957000-223983400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:223957200-223965000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:223957200-223968000	Strong transcription	Brain Germinal Matrix	brain
23	chr1:223957200-223968800	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:223957200-223972800	Strong transcription	Primary B cells from peripheral blood	blood
25	chr1:223958400-223963000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
26	chr1:223958400-223963800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:223958800-223965200	Genic enhancers	Fetal Muscle Leg	muscle
28	chr1:223959200-223964200	Strong transcription	Colon Smooth Muscle	Colon
29	chr1:223959600-223966600	Weak transcription	Fetal Brain Male	brain
30	chr1:223959600-223969000	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:223959800-223977600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:223960000-223963800	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr1:223960000-223964400	Genic enhancers	HSMM	muscle
34	chr1:223960000-223968600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:223960000-223969000	Strong transcription	Fetal Kidney	kidney
36	chr1:223960000-223972200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr1:223960200-223964000	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:223960200-223964000	Genic enhancers	HUVEC	blood vessel
39	chr1:223960200-223964800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:223960200-223970000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:223960200-223971800	Strong transcription	Stomach Smooth Muscle	stomach
42	chr1:223960200-223998600	Strong transcription	Fetal Thymus	thymus
43	chr1:223960200-224025400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:223960400-223964400	Genic enhancers	HSMMtube	muscle
45	chr1:223960400-223968800	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr1:223960600-223967200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:223960600-223986800	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr1:223960600-223995200	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr1:223960600-224001400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr1:223960800-223963000	Weak transcription	Ovary	ovary

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