Variant report

Variant	rs9997299
Chromosome Location	chr4:151138961-151138962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:150920364..150921270-chr4:151137842..151139045,6	MCF-7	breast:
2	chr4:150901416..150902999-chr4:151138902..151140419,2	MCF-7	breast:
3	chr4:150931162..150932721-chr4:151138128..151139077,5	MCF-7	breast:
4	chr4:150931406..150931914-chr4:151138191..151139101,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10019650	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10031796	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12507489	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13107340	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1459744	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1459745	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1459746	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1459747	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1459748	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1459749	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1459751	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1459752	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1563790	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2169086	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2359927	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4025876	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4532220	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs4696241	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6535718	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6535719	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6535720	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6843630	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7658837	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7659254	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7667318	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7699202	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7699907	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9307870	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9307871	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9762327	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9997489	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9999983	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026797	chr4:150246932-151217137	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription 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	12 gene(s)	inside rSNPs	diseases
2	nsv932022	chr4:150831733-151419552	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1032689	chr4:150971003-151316856	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv537300	chr4:150971003-151316856	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv880256	chr4:151126725-151751369	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151114200-151154200	Weak transcription	Aorta	Aorta
2	chr4:151130600-151156000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:151132600-151143200	Weak transcription	Fetal Stomach	stomach
4	chr4:151132800-151150400	Weak transcription	Pancreas	Pancrea
5	chr4:151133200-151145600	Weak transcription	HSMMtube	muscle
6	chr4:151133200-151150400	Weak transcription	Right Ventricle	heart
7	chr4:151133400-151150400	Weak transcription	Fetal Muscle Leg	muscle
8	chr4:151133800-151141000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:151134600-151141600	Weak transcription	HSMM	muscle
10	chr4:151135400-151139600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:151136400-151139800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:151136400-151140000	Enhancers	Fetal Heart	heart
13	chr4:151136400-151141600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr4:151136400-151142200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr4:151136600-151140000	Enhancers	A549	lung
16	chr4:151137000-151146000	Weak transcription	Left Ventricle	heart
17	chr4:151137600-151139600	Enhancers	Fetal Brain Male	brain
18	chr4:151137600-151139800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:151137800-151139000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:151137800-151139600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:151137800-151139600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:151137800-151139800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:151137800-151139800	Enhancers	Brain Anterior Caudate	brain
24	chr4:151138000-151139000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:151138000-151139000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:151138000-151139000	Enhancers	Osteobl	bone
27	chr4:151138000-151139600	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr4:151138000-151139600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr4:151138000-151139800	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr4:151138000-151140000	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr4:151138200-151139000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:151138200-151139000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:151138200-151139000	Enhancers	Muscle Satellite Cultured Cells	--
34	chr4:151138200-151139000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:151138200-151139200	Enhancers	Fetal Brain Female	brain
36	chr4:151138200-151139600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:151138200-151139600	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr4:151138200-151139600	Enhancers	Brain Cingulate Gyrus	brain
39	chr4:151138200-151139800	Enhancers	Fetal Lung	lung
40	chr4:151138400-151149200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr4:151138600-151139000	Enhancers	Adipose Nuclei	Adipose
42	chr4:151138600-151139600	Enhancers	Brain Substantia Nigra	brain
43	chr4:151138600-151139800	Enhancers	Brain Hippocampus Middle	brain
44	chr4:151138600-151145600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr4:151138600-151146000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr4:151138600-151150400	Weak transcription	Ovary	ovary
47	chr4:151138800-151139600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:151138800-151139600	Enhancers	Brain Angular Gyrus	brain
49	chr4:151138800-151139600	Weak transcription	Psoas Muscle	Psoas
50	chr4:151138800-151140000	Enhancers	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links