Variant report

Variant	rs2850981
Chromosome Location	chr4:102097403-102097404
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	chr4:102096828..102098534-chr4:102267844..102269738,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254531	Chromatin interaction
ENSG00000138814	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1021965	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1354785	0.85[ASN][1000 genomes]
rs1395475	0.90[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs1395476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506799	0.85[ASN][1000 genomes]
rs1506800	0.90[CEU][hapmap];0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs1506802	0.85[ASN][1000 genomes]
rs1506803	0.85[ASN][1000 genomes]
rs1506804	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1543856	0.85[ASN][1000 genomes]
rs17030851	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2135610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2135614	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2174683	0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2659503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659505	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659506	0.81[ASN][1000 genomes]
rs2659508	0.89[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2659511	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs2659512	0.90[CEU][hapmap];0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs2659513	0.90[CEU][hapmap];0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs2659522	0.89[CEU][hapmap]
rs2659532	0.84[ASN][1000 genomes]
rs2659533	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs2659534	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs2659538	1.00[CEU][hapmap]
rs2659539	0.85[ASN][1000 genomes]
rs2659540	0.85[ASN][1000 genomes]
rs2659541	0.90[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2850980	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850985	0.82[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2850987	0.90[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2850989	0.88[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs2850991	0.85[ASN][1000 genomes]
rs2850994	0.89[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2850995	0.83[ASN][1000 genomes]
rs3804366	0.89[CEU][hapmap]
rs4478191	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs58879959	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73833252	0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs931871	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer 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 miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102079400-102113800	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr4:102080600-102100600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:102084200-102103400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:102089000-102097600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:102090400-102103800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr4:102090800-102099400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr4:102090800-102112200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:102090800-102114400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr4:102091000-102098400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr4:102091000-102098400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr4:102091200-102103400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr4:102091400-102103600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr4:102093400-102100400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:102093400-102103800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:102093600-102097600	Weak transcription	Stomach Mucosa	stomach
16	chr4:102093600-102103800	Weak transcription	NHEK	skin
17	chr4:102093600-102105200	Weak transcription	NHLF	lung
18	chr4:102093800-102099800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:102094400-102098200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:102094400-102099600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:102094400-102099600	Weak transcription	NHDF-Ad	bronchial
22	chr4:102094400-102103800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:102094400-102108600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:102094600-102100200	Weak transcription	Osteobl	bone
25	chr4:102095800-102097600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:102095800-102098400	Enhancers	Fetal Heart	heart
27	chr4:102095800-102098600	Enhancers	Colon Smooth Muscle	Colon
28	chr4:102095800-102098600	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr4:102095800-102099000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:102095800-102099400	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr4:102095800-102103600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:102096000-102097800	Enhancers	Ovary	ovary
33	chr4:102096200-102112600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:102096400-102097800	Enhancers	Adipose Nuclei	Adipose
35	chr4:102096400-102097800	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr4:102096400-102098600	Enhancers	Rectal Smooth Muscle	rectum
37	chr4:102096600-102097800	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr4:102096600-102098000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr4:102096600-102098400	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr4:102096600-102099200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr4:102096600-102099800	Enhancers	Brain Anterior Caudate	brain
42	chr4:102096600-102112000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr4:102096600-102112000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr4:102096600-102112000	Weak transcription	Right Ventricle	heart
45	chr4:102096800-102097600	Enhancers	Duodenum Mucosa	Duodenum
46	chr4:102096800-102097800	Enhancers	Liver	Liver
47	chr4:102096800-102098600	Enhancers	HepG2	liver
48	chr4:102096800-102099600	Enhancers	HUVEC	blood vessel
49	chr4:102096800-102103400	Weak transcription	Primary B cells from cord blood	blood
50	chr4:102096800-102108000	Weak transcription	Brain Hippocampus Middle	brain

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