Variant report

Variant	rs56287412
Chromosome Location	chr7:17978828-17978829
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:17966773..17969755-chr7:17976526..17979737,3	K562	blood:
2	chr7:17967526..17969640-chr7:17977395..17979886,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10227224	0.82[ASN][1000 genomes]
rs10227582	0.82[ASN][1000 genomes]
rs11768866	0.88[ASN][1000 genomes]
rs12699918	0.89[ASN][1000 genomes]
rs1404424	0.89[ASN][1000 genomes]
rs1524775	0.89[ASN][1000 genomes]
rs1568817	0.80[ASN][1000 genomes]
rs1568818	0.80[ASN][1000 genomes]
rs2103144	0.88[ASN][1000 genomes]
rs2177652	0.81[ASN][1000 genomes]
rs2691555	0.88[ASN][1000 genomes]
rs2691557	0.89[ASN][1000 genomes]
rs2691558	0.80[ASN][1000 genomes]
rs2691559	0.89[ASN][1000 genomes]
rs2691615	0.80[ASN][1000 genomes]
rs2714859	0.80[ASN][1000 genomes]
rs2714869	0.80[ASN][1000 genomes]
rs2723540	0.82[ASN][1000 genomes]
rs35819944	0.88[ASN][1000 genomes]
rs4532510	0.89[ASN][1000 genomes]
rs4543433	0.88[ASN][1000 genomes]
rs4719525	0.83[ASN][1000 genomes]
rs4721671	0.85[ASN][1000 genomes]
rs6955984	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6973480	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9942602	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533938	chr7:17254118-18040301	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1024398	chr7:17630148-18545073	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv538764	chr7:17630148-18545073	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	nsv830913	chr7:17848480-18034218	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1026629	chr7:17862477-18362404	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1025023	chr7:17865796-18357630	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1030201	chr7:17898410-18491985	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
8	nsv887808	chr7:17920613-18150005	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1018517	chr7:17926468-18127372	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv606357	chr7:17938491-18375245	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
11	nsv531013	chr7:17970218-18248642	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
12	nsv1022746	chr7:17978103-18233458	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:17977200-17979400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr7:17977200-17981400	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr7:17977400-17979200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr7:17977400-17979200	Enhancers	Small Intestine	intestine
5	chr7:17977400-17979400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:17977400-17979400	Flanking Active TSS	Dnd41	blood
7	chr7:17977400-17979800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:17977400-17980000	Active TSS	Right Atrium	heart
9	chr7:17977400-17980600	Active TSS	NHLF	lung
10	chr7:17977600-17979200	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr7:17977600-17979400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:17977600-17980800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:17977600-17981200	Active TSS	Right Ventricle	heart
14	chr7:17977800-17979200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr7:17977800-17979200	Flanking Active TSS	NH-A	brain
16	chr7:17977800-17979400	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr7:17977800-17979400	Flanking Active TSS	Liver	Liver
18	chr7:17977800-17980800	Active TSS	GM12878-XiMat	blood
19	chr7:17977800-17981200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr7:17977800-17981200	Active TSS	Stomach Smooth Muscle	stomach
21	chr7:17978000-17979000	Flanking Active TSS	Brain Hippocampus Middle	brain
22	chr7:17978000-17979000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr7:17978000-17979200	Flanking Active TSS	Brain Anterior Caudate	brain
24	chr7:17978000-17979200	Flanking Active TSS	Fetal Brain Female	brain
25	chr7:17978000-17979200	Flanking Active TSS	Fetal Heart	heart
26	chr7:17978000-17979400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr7:17978000-17979800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:17978000-17980000	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr7:17978000-17980000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr7:17978000-17980600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr7:17978000-17980800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr7:17978000-17980800	Active TSS	Hela-S3	cervix
33	chr7:17978000-17981000	Active TSS	Left Ventricle	heart
34	chr7:17978000-17981000	Active TSS	HMEC	breast
35	chr7:17978000-17981200	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr7:17978000-17981200	Active TSS	Brain Angular Gyrus	brain
37	chr7:17978000-17981200	Active TSS	Colonic Mucosa	Colon
38	chr7:17978000-17981200	Active TSS	Fetal Intestine Large	intestine
39	chr7:17978200-17979000	Active TSS	HepG2	liver
40	chr7:17978200-17979200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr7:17978200-17979400	Flanking Active TSS	HUVEC	blood vessel
42	chr7:17978200-17979600	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr7:17978200-17979600	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr7:17978200-17979800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr7:17978200-17980800	Active TSS	Colon Smooth Muscle	Colon
46	chr7:17978200-17980800	Active TSS	HSMMtube	muscle
47	chr7:17978200-17981000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr7:17978200-17981000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr7:17978200-17981000	Active TSS	Fetal Intestine Small	intestine
50	chr7:17978200-17981000	Active TSS	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links