Variant report

Variant	rs61838684
Chromosome Location	chr1:247473889-247473890
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247473800..247482682-chr1:247490121..247498423,19	K562	blood:
2	chr1:247463122..247466119-chr1:247473298..247475329,2	K562	blood:
3	chr1:247473280..247476561-chr1:247492352..247496915,5	MCF-7	breast:
4	chr1:247467380..247471480-chr1:247472464..247476921,4	K562	blood:
5	chr1:247472293..247474768-chr1:247477088..247479599,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162714	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10754543	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10802482	0.83[EUR][1000 genomes]
rs10802483	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11579326	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11579352	0.88[ASN][1000 genomes]
rs11581163	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12081945	0.82[EUR][1000 genomes]
rs12082983	0.88[EUR][1000 genomes]
rs12564303	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12566166	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1771918	0.83[EUR][1000 genomes]
rs17721193	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778552	0.83[EUR][1000 genomes]
rs1778553	0.83[EUR][1000 genomes]
rs2211273	0.89[EUR][1000 genomes]
rs2890342	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41268345	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4925606	0.87[EUR][1000 genomes]
rs4925620	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55686936	0.88[EUR][1000 genomes]
rs55913685	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56124448	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56245379	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56250713	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56358050	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57647632	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57653401	1.00[ASN][1000 genomes]
rs58747962	0.94[ASN][1000 genomes]
rs61838689	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61841570	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426236	0.89[EUR][1000 genomes]
rs6426238	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6656258	0.87[EUR][1000 genomes]
rs6667658	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6698384	0.89[EUR][1000 genomes]
rs6698803	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7544023	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7552041	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[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	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
3	esv3411043	chr1:247382851-247517729	Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
4	esv3378684	chr1:247382994-247518438	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
5	nsv833137	chr1:247437317-247607428	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247456000-247493400	Weak transcription	Right Atrium	heart
2	chr1:247459800-247485800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:247460400-247493400	Strong transcription	Fetal Muscle Leg	muscle
4	chr1:247460800-247474200	Strong transcription	Brain Germinal Matrix	brain
5	chr1:247460800-247474800	Strong transcription	Brain Cingulate Gyrus	brain
6	chr1:247460800-247476200	Weak transcription	HMEC	breast
7	chr1:247460800-247479800	Strong transcription	Fetal Brain Female	brain
8	chr1:247460800-247481000	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:247460800-247491800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:247460800-247493400	Strong transcription	Fetal Muscle Trunk	muscle
11	chr1:247461000-247475400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:247461000-247485400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:247461200-247485400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:247461200-247488200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:247461400-247485400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:247461400-247493800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:247461600-247475200	Strong transcription	Aorta	Aorta
18	chr1:247461600-247481000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:247461800-247474200	Strong transcription	Stomach Smooth Muscle	stomach
20	chr1:247462000-247474000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:247462000-247474000	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr1:247462200-247480000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:247462400-247474000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:247462400-247474400	Strong transcription	Dnd41	blood
25	chr1:247462400-247475600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:247462600-247474000	Strong transcription	Fetal Intestine Small	intestine
27	chr1:247462600-247479200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:247462800-247488000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:247463000-247474000	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr1:247463000-247475000	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr1:247463000-247477000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:247463000-247486200	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:247463000-247486400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:247463000-247493600	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:247463200-247481000	Strong transcription	Left Ventricle	heart
36	chr1:247463200-247493400	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:247463400-247474000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:247463400-247486000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:247463400-247486600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:247464600-247479600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:247464600-247486000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:247464800-247474000	Strong transcription	Fetal Intestine Large	intestine
43	chr1:247464800-247493400	Strong transcription	Fetal Stomach	stomach
44	chr1:247465200-247474000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:247465200-247493400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:247465400-247475000	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:247466800-247474000	Strong transcription	Gastric	stomach
48	chr1:247466800-247485600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr1:247467600-247493800	Weak transcription	Stomach Mucosa	stomach
50	chr1:247467800-247475200	Strong transcription	Fetal Thymus	thymus

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