Variant report

Variant	rs12566716
Chromosome Location	chr1:227950315-227950316
allele	C/T
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:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227668951..227669884-chr1:227949577..227950975,4	MCF-7	breast:
2	chr1:227946182..227953403-chr1:228132950..228136592,12	MCF-7	breast:
3	chr1:227949872..227950667-chr1:228129639..228130594,3	MCF-7	breast:
4	chr1:227945386..227947892-chr1:227948405..227951247,3	MCF-7	breast:
5	chr1:227948959..227950844-chr1:228133923..228134938,14	MCF-7	breast:
6	chr1:227950165..227950767-chr1:227991014..227991675,2	K562	blood:
7	chr1:227913567..227919162-chr1:227947935..227954215,6	MCF-7	breast:
8	chr1:227949868..227950613-chr1:228089588..228090311,2	K562	blood:
9	chr1:227932601..227934786-chr1:227948065..227950535,2	MCF-7	breast:
10	chr1:227950129..227951118-chr1:228133705..228134664,5	MCF-7	breast:
11	chr1:227949923..227950798-chr1:228261303..228262101,2	K562	blood:
12	chr1:227948352..227950485-chr1:227952945..227955700,2	MCF-7	breast:
13	chr1:227636541..227637330-chr1:227949858..227950651,2	K562	blood:
14	chr1:227948805..227951027-chr1:227953567..227955861,2	MCF-7	breast:
15	chr1:227948596..227951213-chr1:228129640..228131293,2	MCF-7	breast:
16	chr1:227918162..227918668-chr1:227949863..227950566,2	MCF-7	breast:
17	chr1:227948253..227951244-chr1:228133555..228136345,5	MCF-7	breast:
18	chr1:227921450..227924362-chr1:227950256..227952147,2	MCF-7	breast:
19	chr1:227950090..227952610-chr1:228122891..228125327,3	MCF-7	breast:
20	chr1:227949885..227950870-chr1:228141682..228142414,6	K562	blood:
21	chr1:227949835..227950876-chr1:228133993..228134931,7	K562	blood:
22	chr1:227949805..227950774-chr1:227975453..227976341,2	K562	blood:
23	chr1:227949947..227950738-chr17:18770247..18771173,2	MCF-7	breast:
24	chr1:227915843..227918254-chr1:227950169..227951754,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143740	Chromatin interaction
ENSG00000081692	Chromatin interaction
ENSG00000143816	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12563117	1.00[EUR][1000 genomes]
rs12563564	1.00[EUR][1000 genomes]
rs12564736	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564917	1.00[EUR][1000 genomes]
rs12564929	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12565099	1.00[EUR][1000 genomes]
rs12565109	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12565618	1.00[EUR][1000 genomes]
rs12565653	1.00[EUR][1000 genomes]
rs12566390	1.00[EUR][1000 genomes]
rs12566948	1.00[ASN][1000 genomes]
rs12567084	1.00[EUR][1000 genomes]
rs12567160	1.00[EUR][1000 genomes]
rs12567934	1.00[EUR][1000 genomes]
rs12568707	1.00[EUR][1000 genomes]
rs1323021	1.00[EUR][1000 genomes]
rs13373816	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16841323	1.00[EUR][1000 genomes]
rs16847987	1.00[EUR][1000 genomes]
rs16848026	1.00[EUR][1000 genomes]
rs16848044	1.00[EUR][1000 genomes]
rs16848160	1.00[EUR][1000 genomes]
rs17492440	1.00[EUR][1000 genomes]
rs17492447	1.00[EUR][1000 genomes]
rs2101862	1.00[EUR][1000 genomes]
rs2313220	1.00[EUR][1000 genomes]
rs34984248	1.00[EUR][1000 genomes]
rs35703429	1.00[EUR][1000 genomes]
rs41305134	1.00[ASN][1000 genomes]
rs4462138	1.00[EUR][1000 genomes]
rs60156730	1.00[ASN][1000 genomes]
rs61827011	1.00[AFR][1000 genomes]
rs6665512	1.00[EUR][1000 genomes]
rs6684706	1.00[ASN][1000 genomes]
rs73090985	1.00[EUR][1000 genomes]
rs73090986	1.00[EUR][1000 genomes]
rs73090987	1.00[EUR][1000 genomes]
rs73090994	1.00[EUR][1000 genomes]
rs73091000	1.00[EUR][1000 genomes]
rs73092607	1.00[EUR][1000 genomes]
rs73092610	1.00[EUR][1000 genomes]
rs996226	1.00[EUR][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

No data

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	chr1:227934800-227950400	Strong transcription	Fetal Intestine Small	intestine
3	chr1:227938600-227950400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:227944000-227950400	Strong transcription	Fetal Intestine Large	intestine
5	chr1:227944000-227951800	Genic enhancers	Fetal Muscle Leg	muscle
6	chr1:227945800-227954800	Weak transcription	Fetal Kidney	kidney
7	chr1:227946000-227950600	Genic enhancers	GM12878-XiMat	blood
8	chr1:227946000-227960400	Strong transcription	Fetal Brain Female	brain
9	chr1:227946800-227952400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:227947600-227954800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:227947800-227950400	Weak transcription	HUVEC	blood vessel
12	chr1:227947800-227951600	Enhancers	Fetal Heart	heart
13	chr1:227947800-227955400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:227948000-227950400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:227948000-227950400	Strong transcription	Fetal Stomach	stomach
16	chr1:227948000-227953600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:227948200-227952200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
18	chr1:227948200-227954600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:227948400-227955400	Weak transcription	Psoas Muscle	Psoas
20	chr1:227948400-227956000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr1:227948600-227955600	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr1:227948800-227952800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:227949000-227950400	Strong transcription	NHLF	lung
24	chr1:227949000-227953400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:227949200-227951000	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr1:227949200-227951200	Genic enhancers	Colonic Mucosa	Colon
27	chr1:227949200-227951200	Genic enhancers	Gastric	stomach
28	chr1:227949200-227951800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr1:227949200-227952200	Genic enhancers	Esophagus	oesophagus
30	chr1:227949200-227954400	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr1:227949200-227954800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:227949200-227956000	Genic enhancers	Fetal Thymus	thymus
33	chr1:227949400-227950400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:227949400-227950400	Genic enhancers	Spleen	Spleen
35	chr1:227949400-227950600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr1:227949400-227952200	Genic enhancers	Fetal Muscle Trunk	muscle
37	chr1:227949400-227954200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:227949400-227954400	Enhancers	Placenta Amnion	Placenta Amnion
39	chr1:227949400-227954600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:227949600-227950400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr1:227949600-227950400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:227949600-227951000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:227949600-227951200	Genic enhancers	Dnd41	blood
44	chr1:227949600-227951800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:227949600-227952800	Enhancers	HMEC	breast
46	chr1:227949600-227953400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr1:227949600-227954400	Weak transcription	Brain Substantia Nigra	brain
48	chr1:227949600-227955400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:227949600-227955600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:227949800-227950400	Enhancers	Adipose Nuclei	Adipose

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