Variant report

Variant	rs10404945
Chromosome Location	chr19:38022358-38022359
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1015848	0.84[EUR][1000 genomes]
rs1015849	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs10403582	0.82[EUR][1000 genomes]
rs10404920	0.93[CEU][hapmap]
rs10405064	0.93[CEU][hapmap]
rs10405407	0.93[CEU][hapmap]
rs10406177	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs10407084	0.93[CEU][hapmap]
rs10409204	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs10411574	0.91[EUR][1000 genomes]
rs10414904	0.93[CEU][hapmap]
rs10415937	0.93[CEU][hapmap]
rs10417503	0.93[CEU][hapmap]
rs10417844	0.86[CEU][hapmap]
rs10420722	0.86[EUR][1000 genomes]
rs10420754	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs10422667	0.84[EUR][1000 genomes]
rs10424574	0.93[CEU][hapmap]
rs10426618	0.84[EUR][1000 genomes]
rs11083426	0.96[EUR][1000 genomes]
rs12972252	0.84[EUR][1000 genomes]
rs12979470	0.83[EUR][1000 genomes]
rs13343471	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs13343502	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs13345116	0.93[CEU][hapmap]
rs1373991	0.93[CEU][hapmap]
rs1382357	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs1559229	0.93[CEU][hapmap]
rs2045908	0.90[EUR][1000 genomes]
rs2081096	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs2112922	0.82[EUR][1000 genomes]
rs2112923	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs2126977	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[EUR][1000 genomes]
rs2279148	1.00[CEU][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes]
rs2279149	1.00[CEU][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes]
rs2291004	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2303131	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs28373708	0.90[EUR][1000 genomes]
rs28538699	0.85[EUR][1000 genomes]
rs28605784	0.88[EUR][1000 genomes]
rs28623164	0.83[EUR][1000 genomes]
rs2891699	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs35540940	0.92[EUR][1000 genomes]
rs35777021	0.82[EUR][1000 genomes]
rs3745765	0.93[CEU][hapmap]
rs3760825	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs4417644	0.93[CEU][hapmap]
rs4452075	0.93[CEU][hapmap]
rs4801759	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs4801803	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs4802766	0.87[EUR][1000 genomes]
rs4802889	0.90[EUR][1000 genomes]
rs4803195	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4803210	0.88[CEU][hapmap]
rs4803229	0.93[CEU][hapmap]
rs59224125	0.86[EUR][1000 genomes]
rs6508719	0.93[CEU][hapmap]
rs6508732	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[EUR][1000 genomes]
rs6508733	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[EUR][1000 genomes]
rs713256	0.93[CEU][hapmap]
rs7247259	0.93[CEU][hapmap]
rs7248733	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[EUR][1000 genomes]
rs7252099	0.82[EUR][1000 genomes]
rs7252325	0.83[EUR][1000 genomes]
rs7252346	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs7253091	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs7253114	1.00[CEU][hapmap];0.96[YRI][hapmap];0.93[EUR][1000 genomes]
rs7255407	0.83[EUR][1000 genomes]
rs7255785	0.87[EUR][1000 genomes]
rs7255952	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7255972	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs7255996	0.87[EUR][1000 genomes]
rs7257672	0.93[CEU][hapmap]
rs73631095	0.87[EUR][1000 genomes]
rs8106839	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs8109038	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs8109632	0.83[EUR][1000 genomes]
rs8111782	0.93[CEU][hapmap]
rs9304566	0.93[CEU][hapmap]
rs9676739	0.85[EUR][1000 genomes]
rs9676967	0.83[EUR][1000 genomes]
rs9917081	0.93[CEU][hapmap]

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	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv833819	chr19:37899501-38051599	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37998800-38022600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:37999000-38028800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:38002000-38028800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
4	chr19:38008800-38026600	Weak transcription	Fetal Heart	heart
5	chr19:38011600-38023600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:38014800-38024000	Weak transcription	Stomach Mucosa	stomach
7	chr19:38015800-38022600	Weak transcription	Fetal Kidney	kidney
8	chr19:38017400-38028800	ZNF genes & repeats	Adipose Nuclei	Adipose
9	chr19:38017600-38022400	Weak transcription	Fetal Lung	lung
10	chr19:38017800-38023800	Weak transcription	Placenta	Placenta
11	chr19:38017800-38024000	Strong transcription	Brain Hippocampus Middle	brain
12	chr19:38018400-38025000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:38020000-38022400	Weak transcription	Psoas Muscle	Psoas
14	chr19:38020000-38023800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr19:38020000-38024000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:38020200-38022400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:38020200-38022400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:38020400-38022400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr19:38020400-38022400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr19:38020400-38022400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr19:38020400-38022400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr19:38020400-38022400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr19:38020400-38022400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr19:38020400-38022400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr19:38020400-38022600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:38020400-38022600	Weak transcription	Brain Angular Gyrus	brain
27	chr19:38020400-38022600	Weak transcription	Colon Smooth Muscle	Colon
28	chr19:38020600-38022400	Weak transcription	Fetal Brain Male	brain
29	chr19:38020800-38022400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr19:38020800-38022400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:38020800-38022400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr19:38020800-38022400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr19:38020800-38022400	Weak transcription	Brain Germinal Matrix	brain
34	chr19:38020800-38022400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr19:38020800-38022400	Weak transcription	Gastric	stomach
36	chr19:38020800-38022400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr19:38020800-38022600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr19:38020800-38022600	Weak transcription	Brain Anterior Caudate	brain
39	chr19:38020800-38023000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr19:38020800-38023000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr19:38021400-38022600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
42	chr19:38021600-38024000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr19:38021600-38028800	ZNF genes & repeats	Primary T cells from cord blood	blood
44	chr19:38021600-38030200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
45	chr19:38021800-38022600	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr19:38021800-38022800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
47	chr19:38021800-38023400	Strong transcription	Fetal Brain Female	brain
48	chr19:38021800-38023800	Strong transcription	Brain Substantia Nigra	brain
49	chr19:38021800-38028800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
50	chr19:38021800-38028800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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