Variant report

Variant	rs1838207
Chromosome Location	chr5:112621104-112621105
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112619318..112622139-chr5:112627969..112630686,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171444	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10042223	0.81[CHB][hapmap]
rs10051834	0.81[CHB][hapmap]
rs10067046	0.85[CEU][hapmap]
rs10072511	0.86[CEU][hapmap]
rs10074214	0.81[CHB][hapmap]
rs1038918	0.84[CEU][hapmap]
rs10900684	0.85[CEU][hapmap]
rs11241200	0.85[CEU][hapmap]
rs13153071	0.85[CEU][hapmap]
rs13188946	0.81[CHB][hapmap]
rs13190054	0.96[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1517208	0.84[AMR][1000 genomes]
rs1517210	0.87[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes]
rs154039	0.81[AMR][1000 genomes]
rs154040	0.83[AMR][1000 genomes]
rs164251	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs173903	0.81[AMR][1000 genomes]
rs1845290	0.87[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes]
rs2222144	0.81[CHB][hapmap]
rs2416310	0.86[CEU][hapmap]
rs255856	0.87[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes]
rs255858	0.84[AMR][1000 genomes]
rs255863	0.82[AMR][1000 genomes]
rs255867	0.85[AMR][1000 genomes]
rs255874	0.83[AMR][1000 genomes]
rs26960	0.84[AMR][1000 genomes]
rs26985	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs27566	0.87[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes]
rs27567	0.81[CHB][hapmap]
rs3857435	0.81[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes]
rs4331889	0.81[CHB][hapmap]
rs4398627	0.80[CHB][hapmap]
rs461034	0.87[CHB][hapmap]
rs463216	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs465898	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs466564	0.83[JPT][hapmap]
rs4705812	0.85[CEU][hapmap]
rs4705813	0.86[AMR][1000 genomes]
rs485210	0.88[AMR][1000 genomes]
rs492346	0.89[AMR][1000 genomes]
rs6594704	0.81[CHB][hapmap]
rs6594705	0.81[CHB][hapmap]
rs6594710	0.81[CHB][hapmap]
rs6594711	0.83[JPT][hapmap];0.84[AMR][1000 genomes]
rs6594712	0.81[CHB][hapmap]
rs675353	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs6867397	0.81[CHB][hapmap]
rs6869097	0.89[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6873400	0.84[CEU][hapmap]
rs6875238	0.86[AMR][1000 genomes]
rs7702120	0.81[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes]
rs7708084	0.81[CHB][hapmap]
rs7715342	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7722276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7725589	0.81[CHB][hapmap]
rs7731465	0.81[CHB][hapmap]
rs7735247	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1024747	chr5:112592710-112679373	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1018078	chr5:112615220-112657404	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv949165	chr5:112615626-112730216	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112586600-112623600	Weak transcription	Pancreas	Pancrea
2	chr5:112608000-112628200	Weak transcription	HMEC	breast
3	chr5:112610000-112628200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:112610800-112623200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:112611000-112628200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:112612000-112623800	Weak transcription	Fetal Muscle Leg	muscle
7	chr5:112612000-112625200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:112612200-112625200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:112614200-112625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:112615000-112625200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:112616800-112623400	Weak transcription	NHEK	skin
12	chr5:112616800-112623800	Weak transcription	Esophagus	oesophagus
13	chr5:112617000-112622000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:112617200-112621200	Weak transcription	Psoas Muscle	Psoas
15	chr5:112617400-112621600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:112617800-112625400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:112617800-112628600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr5:112618200-112623600	Weak transcription	Gastric	stomach
19	chr5:112618400-112621200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:112618400-112621200	Weak transcription	Adipose Nuclei	Adipose
21	chr5:112618400-112628000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:112618400-112628200	Weak transcription	Fetal Kidney	kidney
23	chr5:112618400-112628200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr5:112618400-112628400	Weak transcription	Fetal Stomach	stomach
25	chr5:112618600-112625600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:112618800-112621200	Weak transcription	Right Ventricle	heart
27	chr5:112618800-112622000	Weak transcription	Brain Angular Gyrus	brain
28	chr5:112619000-112621200	Weak transcription	Left Ventricle	heart
29	chr5:112619000-112626800	Weak transcription	Liver	Liver
30	chr5:112619000-112628600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:112619000-112628800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr5:112619200-112625600	Weak transcription	Fetal Lung	lung
33	chr5:112619400-112621800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:112619400-112624000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr5:112619400-112625200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr5:112619600-112621200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr5:112619600-112625200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr5:112619800-112621600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr5:112620000-112621200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr5:112620000-112621200	Weak transcription	Right Atrium	heart
41	chr5:112620000-112621600	Weak transcription	Fetal Heart	heart
42	chr5:112620000-112628200	Weak transcription	Brain Anterior Caudate	brain
43	chr5:112620000-112628200	Weak transcription	Brain Cingulate Gyrus	brain
44	chr5:112620200-112621200	Weak transcription	Brain Substantia Nigra	brain
45	chr5:112620400-112621600	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr5:112620400-112625200	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr5:112621000-112621200	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr5:112621000-112622400	Enhancers	Ovary	ovary

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