Variant report

Variant	rs1123897
Chromosome Location	chr3:120157034-120157035
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120136351..120139286-chr3:120156446..120159592,3	MCF-7	breast:
2	chr3:120155958..120158506-chr3:120167784..120170951,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163430	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1123898	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1147709	0.89[CHB][hapmap];0.81[LWK][hapmap]
rs1147720	0.88[CHB][hapmap]
rs1259311	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1259318	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs1259329	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1259331	0.94[CHB][hapmap]
rs1259332	0.94[CHB][hapmap]
rs1259333	0.85[JPT][hapmap]
rs1259334	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.98[ASN][1000 genomes]
rs1259335	0.83[JPT][hapmap]
rs1259336	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1259337	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.83[YRI][hapmap];0.97[ASN][1000 genomes]
rs1259338	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.98[ASN][1000 genomes]
rs1259339	0.94[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs1267675	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.83[YRI][hapmap];0.98[ASN][1000 genomes]
rs1270209	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1520881	0.87[ASW][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.84[LWK][hapmap]
rs1716835	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1733296	0.88[CHB][hapmap]
rs1733299	0.97[ASN][1000 genomes]
rs1733304	0.87[ASW][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.84[LWK][hapmap]
rs1733306	0.94[CHB][hapmap]
rs1733319	0.93[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2252084	0.94[CHB][hapmap]
rs2700263	0.88[ASN][1000 genomes]
rs2702155	0.89[CHB][hapmap]
rs6764364	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs6791913	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs874477	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs874479	0.94[CHB][hapmap];0.81[CHD][hapmap]
rs874480	0.98[ASN][1000 genomes]
rs9631455	0.93[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9854823	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs9855400	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs9879383	0.95[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active 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 miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120137400-120162200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr3:120137800-120161600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:120138200-120157200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:120138200-120162000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:120138200-120167800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:120138200-120169200	Weak transcription	Gastric	stomach
7	chr3:120144400-120165800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:120145400-120157600	Weak transcription	Fetal Brain Female	brain
9	chr3:120145800-120168800	Weak transcription	Pancreas	Pancrea
10	chr3:120146800-120157800	Weak transcription	Fetal Brain Male	brain
11	chr3:120148000-120161000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:120149000-120161200	Genic enhancers	NHDF-Ad	bronchial
13	chr3:120149400-120157200	Weak transcription	Colonic Mucosa	Colon
14	chr3:120150400-120157400	Weak transcription	Fetal Intestine Large	intestine
15	chr3:120151800-120166200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:120152000-120158400	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:120152200-120157200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:120152600-120161400	Genic enhancers	Fetal Muscle Leg	muscle
19	chr3:120152600-120162200	Genic enhancers	Fetal Stomach	stomach
20	chr3:120153000-120157600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr3:120153000-120167600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:120153200-120159400	Weak transcription	Spleen	Spleen
23	chr3:120153400-120160600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:120153800-120159400	Enhancers	Aorta	Aorta
25	chr3:120154000-120161200	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr3:120154200-120157600	Enhancers	Rectal Smooth Muscle	rectum
27	chr3:120154200-120159600	Genic enhancers	HSMM	muscle
28	chr3:120154400-120160400	Weak transcription	Brain Angular Gyrus	brain
29	chr3:120154600-120157600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:120154600-120157600	Weak transcription	Stomach Mucosa	stomach
31	chr3:120154600-120158000	Weak transcription	Psoas Muscle	Psoas
32	chr3:120154800-120157400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:120154800-120157600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:120154800-120158400	Weak transcription	Fetal Intestine Small	intestine
35	chr3:120155000-120157400	Weak transcription	Fetal Kidney	kidney
36	chr3:120155200-120157200	Genic enhancers	Stomach Smooth Muscle	stomach
37	chr3:120155200-120160200	Genic enhancers	HSMMtube	muscle
38	chr3:120155200-120163400	Genic enhancers	NHLF	lung
39	chr3:120155400-120157400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr3:120155400-120159200	Weak transcription	HMEC	breast
41	chr3:120155400-120160800	Genic enhancers	Muscle Satellite Cultured Cells	--
42	chr3:120155400-120161400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr3:120155400-120162800	Enhancers	Right Atrium	heart
44	chr3:120155600-120157200	Genic enhancers	NH-A	brain
45	chr3:120155600-120157600	Genic enhancers	HUVEC	blood vessel
46	chr3:120155600-120160600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:120155800-120157200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr3:120155800-120157600	Weak transcription	NHEK	skin
49	chr3:120155800-120157800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:120155800-120157800	Genic enhancers	Adipose Nuclei	Adipose

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