Variant report

Variant	rs7618573
Chromosome Location	chr3:52116714-52116715
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	chr3:52108818..52113062-chr3:52113432..52117079,5	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12485855	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12488456	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12489539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12493204	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17051963	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3821841	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3852069	0.81[AMR][1000 genomes]
rs4687608	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs4687609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4687798	0.81[MEX][hapmap]
rs4687801	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687802	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687806	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4687808	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4687809	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66530305	0.83[AMR][1000 genomes]
rs72622937	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs747343	0.83[MEX][hapmap]
rs920160	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9637473	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9873175	0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
6	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52097600-52119800	Weak transcription	GM12878-XiMat	blood
2	chr3:52102600-52121000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:52103200-52122000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr3:52103200-52124800	Weak transcription	Colonic Mucosa	Colon
5	chr3:52105600-52119600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:52105600-52120800	Strong transcription	Dnd41	blood
7	chr3:52105600-52124000	Weak transcription	Pancreas	Pancrea
8	chr3:52105800-52119200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:52105800-52124000	Weak transcription	Hela-S3	cervix
10	chr3:52105800-52142400	Weak transcription	Primary B cells from cord blood	blood
11	chr3:52106200-52121000	Weak transcription	HSMM	muscle
12	chr3:52107200-52123200	Weak transcription	Fetal Brain Female	brain
13	chr3:52108800-52122200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:52109600-52123800	Weak transcription	NHEK	skin
15	chr3:52109600-52129800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:52110000-52120000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr3:52110000-52121600	Weak transcription	NHLF	lung
18	chr3:52110000-52122000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:52110000-52125000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:52110000-52126000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:52110000-52126000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:52110000-52127000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:52110000-52127200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:52110000-52127400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:52110200-52125400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:52110600-52179400	Weak transcription	Brain Germinal Matrix	brain
27	chr3:52110800-52122400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:52111200-52122200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:52111200-52127000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:52111600-52120600	Weak transcription	Lung	lung
31	chr3:52111600-52120800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr3:52111600-52120800	Weak transcription	Right Atrium	heart
33	chr3:52112200-52121000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:52112400-52118800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:52112400-52120600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:52112400-52120600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:52112400-52122200	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:52113200-52119000	Weak transcription	Fetal Muscle Leg	muscle
39	chr3:52113200-52119800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:52113400-52118400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:52113800-52116800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:52113800-52119600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:52114000-52119200	Weak transcription	Fetal Muscle Trunk	muscle
44	chr3:52114400-52118600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:52114800-52118400	Weak transcription	Fetal Thymus	thymus
46	chr3:52114800-52118600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:52115000-52117400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:52115000-52119200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:52115600-52117800	Weak transcription	Fetal Intestine Small	intestine
50	chr3:52115600-52120600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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