Variant report

Variant	rs1801
Chromosome Location	chr4:103501054-103501055
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	chr4:103421751..103424038-chr4:103500019..103502227,2	MCF-7	breast:
2	chr4:103419957..103425638-chr4:103495824..103504548,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109320	Chromatin interaction
ENSG00000260651	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1005819	1.00[JPT][hapmap]
rs1020759	0.90[JPT][hapmap]
rs1020760	1.00[JPT][hapmap]
rs11722146	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11723120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs118882	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs12509403	0.93[YRI][hapmap]
rs12509517	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12648696	0.94[CHB][hapmap]
rs1585213	0.91[JPT][hapmap]
rs1585215	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs1598859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1599961	0.91[JPT][hapmap]
rs1609798	0.82[CHB][hapmap]
rs17032705	0.91[JPT][hapmap]
rs170731	0.86[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2168805	0.86[JPT][hapmap]
rs230491	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230492	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230493	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230495	0.91[JPT][hapmap]
rs230496	0.91[JPT][hapmap]
rs230498	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs230500	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs230504	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230505	0.91[JPT][hapmap]
rs230509	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230511	0.86[CEU][hapmap]
rs230514	0.86[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230515	0.82[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs230516	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs230519	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230520	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230521	0.91[JPT][hapmap]
rs230525	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230526	0.91[JPT][hapmap]
rs230528	0.91[JPT][hapmap]
rs230529	0.91[JPT][hapmap]
rs230531	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230532	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230533	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230534	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230535	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230539	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs230540	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230541	1.00[JPT][hapmap]
rs230542	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3755867	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3774933	0.91[JPT][hapmap]
rs3774936	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs3774937	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs3774938	0.91[JPT][hapmap]
rs3774956	1.00[JPT][hapmap]
rs3774959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3774963	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs3774964	1.00[JPT][hapmap]
rs3817685	1.00[JPT][hapmap]
rs3821958	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs4235404	0.85[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]
rs4648011	0.91[JPT][hapmap]
rs4648055	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4648058	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs4648068	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4648133	0.86[CHB][hapmap]
rs4698858	1.00[JPT][hapmap]
rs4698861	0.81[JPT][hapmap]
rs4698863	0.82[JPT][hapmap]
rs4699030	1.00[JPT][hapmap]
rs747559	0.91[JPT][hapmap]
rs9790601	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs980455	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830020	chr4:103387343-103581284	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1003490	chr4:103391483-103521772	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1004030	chr4:103419352-103504042	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv537203	chr4:103419352-103504042	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103473400-103524600	Weak transcription	Fetal Brain Male	brain
2	chr4:103478200-103511800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:103483000-103518600	Weak transcription	Small Intestine	intestine
4	chr4:103483200-103516600	Weak transcription	Brain Angular Gyrus	brain
5	chr4:103483400-103541600	Weak transcription	K562	blood
6	chr4:103488200-103520000	Weak transcription	Fetal Kidney	kidney
7	chr4:103490800-103519200	Weak transcription	Stomach Mucosa	stomach
8	chr4:103495800-103511800	Strong transcription	Primary B cells from cord blood	blood
9	chr4:103495800-103516400	Weak transcription	NHLF	lung
10	chr4:103496200-103513200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr4:103496400-103510000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:103497000-103504000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr4:103497000-103516600	Weak transcription	Brain Substantia Nigra	brain
14	chr4:103497400-103513000	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr4:103497600-103504800	Strong transcription	Stomach Smooth Muscle	stomach
16	chr4:103497600-103505200	Strong transcription	Primary hematopoietic stem cells	blood
17	chr4:103497600-103505400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr4:103497600-103506600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr4:103497600-103507000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr4:103497600-103533400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr4:103497800-103501400	Strong transcription	Fetal Intestine Large	intestine
22	chr4:103497800-103505800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:103497800-103505800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:103497800-103506200	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr4:103497800-103509400	Strong transcription	Fetal Muscle Trunk	muscle
26	chr4:103497800-103509400	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr4:103498000-103502000	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:103498000-103503400	Strong transcription	HSMMtube	muscle
29	chr4:103498000-103504800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:103498000-103506000	Strong transcription	NHEK	skin
31	chr4:103498000-103507000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:103498000-103507200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr4:103498000-103508200	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr4:103498000-103509000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr4:103498000-103509600	Strong transcription	Duodenum Mucosa	Duodenum
36	chr4:103498000-103510200	Strong transcription	Adipose Nuclei	Adipose
37	chr4:103498000-103511600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:103498000-103511600	Strong transcription	Dnd41	blood
39	chr4:103498000-103513000	Strong transcription	Liver	Liver
40	chr4:103498000-103513200	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr4:103498200-103502200	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr4:103498200-103511600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:103498200-103513400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:103498200-103513600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:103498600-103502600	Weak transcription	NHDF-Ad	bronchial
46	chr4:103498600-103507400	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr4:103498800-103501200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:103498800-103502000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr4:103498800-103502000	Enhancers	Fetal Heart	heart
50	chr4:103498800-103520600	Weak transcription	Fetal Brain Female	brain

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