Variant report

Variant	rs10029528
Chromosome Location	chr4:99430799-99430800
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:99422257..99425679-chr4:99427577..99430821,3	MCF-7	breast:
2	chr4:99428008..99431537-chr4:99432874..99435399,3	MCF-7	breast:
3	chr4:99422565..99426189-chr4:99427302..99431103,4	K562	blood:
4	chr4:99429986..99431627-chr4:99434644..99437032,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10005706	1.00[CEU][hapmap]
rs10007752	1.00[CEU][hapmap]
rs10010485	0.86[EUR][1000 genomes]
rs10030396	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10031904	1.00[CEU][hapmap]
rs10032578	1.00[CEU][hapmap]
rs12233846	1.00[JPT][hapmap]
rs17027682	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17027707	1.00[CEU][hapmap]
rs17027758	1.00[CEU][hapmap]
rs17027760	1.00[CEU][hapmap]
rs17027826	1.00[CEU][hapmap]
rs17027841	1.00[CEU][hapmap]
rs17027845	1.00[CEU][hapmap]
rs1919212	0.86[EUR][1000 genomes]
rs28372028	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs28420592	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28483089	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28502504	0.86[EUR][1000 genomes]
rs28504661	0.86[EUR][1000 genomes]
rs28532945	0.89[EUR][1000 genomes]
rs28550027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28648419	0.86[EUR][1000 genomes]
rs28704122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28712025	0.86[EUR][1000 genomes]
rs28758777	0.86[EUR][1000 genomes]
rs9990571	0.86[EUR][1000 genomes]
rs9991086	0.86[EUR][1000 genomes]

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	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv879651	chr4:99105055-99441349	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1004181	chr4:99208152-99529576	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99396200-99431400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr4:99397600-99439400	Weak transcription	Primary B cells from cord blood	blood
3	chr4:99405600-99431000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr4:99408000-99432200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr4:99409800-99431600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr4:99416200-99431600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr4:99416600-99430800	Weak transcription	Thymus	Thymus
8	chr4:99417200-99431200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:99417800-99438600	Weak transcription	Right Atrium	heart
10	chr4:99419600-99436400	Weak transcription	HUVEC	blood vessel
11	chr4:99420200-99435800	Weak transcription	Spleen	Spleen
12	chr4:99420400-99431000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:99420400-99436400	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr4:99420400-99436400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr4:99423000-99434200	Weak transcription	Aorta	Aorta
16	chr4:99423000-99434200	Weak transcription	Esophagus	oesophagus
17	chr4:99423800-99431000	Weak transcription	NHEK	skin
18	chr4:99424600-99431000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:99424800-99430800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:99424800-99431200	Weak transcription	Primary T cells from cord blood	blood
21	chr4:99425000-99436200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr4:99425600-99434200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:99425800-99431000	Weak transcription	Fetal Thymus	thymus
24	chr4:99427800-99432800	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr4:99428000-99431600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr4:99428200-99432000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:99429200-99431200	Enhancers	Fetal Brain Male	brain
28	chr4:99429200-99432600	Enhancers	Ovary	ovary
29	chr4:99429800-99432000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:99429800-99432400	Enhancers	Fetal Muscle Leg	muscle
31	chr4:99429800-99432600	Enhancers	NH-A	brain
32	chr4:99430000-99431800	Enhancers	Fetal Heart	heart
33	chr4:99430000-99432200	Enhancers	Brain Angular Gyrus	brain
34	chr4:99430000-99432600	Enhancers	Brain Hippocampus Middle	brain
35	chr4:99430000-99432800	Enhancers	Muscle Satellite Cultured Cells	--
36	chr4:99430000-99432800	Enhancers	Fetal Lung	lung
37	chr4:99430000-99432800	Enhancers	NHLF	lung
38	chr4:99430200-99431000	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr4:99430200-99431000	Flanking Active TSS	NHDF-Ad	bronchial
40	chr4:99430200-99431400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:99430200-99431400	Enhancers	Brain Germinal Matrix	brain
42	chr4:99430200-99431400	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr4:99430200-99431600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:99430200-99431600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr4:99430200-99431600	Enhancers	Fetal Brain Female	brain
46	chr4:99430200-99432000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr4:99430200-99432400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr4:99430200-99432600	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr4:99430200-99432600	Enhancers	Brain Cingulate Gyrus	brain
50	chr4:99430200-99432600	Enhancers	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links