Variant report

Variant	rs10494588
Chromosome Location	chr1:186382826-186382827
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr1:186382325-186383044	SK-N-SH	brain:	n/a	chr1:186382822-186382836
2	GATA3	chr1:186382597-186382971	SH-SY5Y	brain:	n/a	n/a
3	FOSL2	chr1:186382385-186382869	SK-N-SH	brain:	n/a	n/a
4	JUND	chr1:186382382-186382931	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr1:186382267-186383254	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr1:186382398-186383095	SK-N-SH	brain:	n/a	n/a
7	GATA2	chr1:186382468-186383233	HUVEC	blood vessel:	n/a	n/a
8	FOS	chr1:186382446-186382849	HUVEC	blood vessel:	n/a	n/a
9	GATA3	chr1:186382337-186383252	SK-N-SH	brain:	n/a	n/a
10	NFIC	chr1:186382380-186383082	SK-N-SH	brain:	n/a	n/a
11	JUND	chr1:186382344-186382932	SK-N-SH	brain:	n/a	n/a
12	IRF1	chr1:186382567-186382839	K562	blood:	n/a	n/a
13	PBX3	chr1:186382418-186382910	SK-N-SH	brain:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:186378179..186381084-chr1:186382062..186384973,3	K562	blood:
2	chr1:186343907..186345654-chr1:186382510..186384256,2	MCF-7	breast:
3	chr1:186378179..186381084-chr1:186382062..186384910,2	K562	blood:
4	chr1:186381482..186384419-chr1:186389970..186392449,3	K562	blood:

No data

Variant related genes	Relation type
C1orf27	TF binding region
ENSG00000157181	Chromatin interaction
ENSG00000047410	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10158395	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs10489394	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10489395	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10494585	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12239322	0.87[AFR][1000 genomes]
rs13374242	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13375943	1.00[YRI][hapmap]
rs13376114	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs16825179	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs16825187	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16825230	0.81[AMR][1000 genomes]
rs16825277	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16825282	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16825292	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16825329	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16825448	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs16825457	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1929094	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2141392	0.84[YRI][hapmap]
rs3934201	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs41393449	0.87[AFR][1000 genomes]
rs56158125	0.83[AFR][1000 genomes]
rs56888492	0.89[AMR][1000 genomes]
rs57020506	0.91[AFR][1000 genomes]
rs59886878	0.87[AFR][1000 genomes]
rs60957652	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6425029	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6673816	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6679283	0.91[AFR][1000 genomes]
rs6688055	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6695920	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7355203	0.89[AMR][1000 genomes]
rs7530502	0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7547924	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1822818	chr1:186301447-186441585	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1012164	chr1:186323867-186565995	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv2762201	chr1:186323879-186566007	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv872589	chr1:186354146-186390303	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	esv1824284	chr1:186358588-186441585	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186345400-186390600	Weak transcription	Small Intestine	intestine
2	chr1:186345400-186398200	Weak transcription	Spleen	Spleen
3	chr1:186346200-186388400	Weak transcription	Colonic Mucosa	Colon
4	chr1:186346400-186388000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:186346400-186390000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:186348600-186390200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:186361600-186388400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:186362400-186405600	Weak transcription	Brain Angular Gyrus	brain
9	chr1:186362800-186405600	Weak transcription	Right Ventricle	heart
10	chr1:186365400-186390200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:186365600-186388000	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:186365600-186395200	Weak transcription	Psoas Muscle	Psoas
13	chr1:186365800-186388000	Weak transcription	Aorta	Aorta
14	chr1:186365800-186388000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:186365800-186388000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:186366200-186393800	Weak transcription	Lung	lung
17	chr1:186366400-186388000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:186367600-186390000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:186367800-186387800	Weak transcription	Fetal Brain Male	brain
20	chr1:186368200-186388000	Weak transcription	Brain Substantia Nigra	brain
21	chr1:186368600-186398200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:186368800-186387800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:186370400-186388200	Weak transcription	HSMMtube	muscle
24	chr1:186370600-186388000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:186371400-186383000	Strong transcription	HSMM	muscle
26	chr1:186371600-186383000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:186371600-186383200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:186372000-186389400	Weak transcription	Gastric	stomach
29	chr1:186372000-186391000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:186372000-186392000	Weak transcription	Esophagus	oesophagus
31	chr1:186372000-186398200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:186372000-186406000	Weak transcription	Pancreas	Pancrea
33	chr1:186373200-186383400	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:186374200-186383000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:186374400-186383200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:186374400-186383200	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr1:186374400-186383200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr1:186374600-186383000	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr1:186374800-186383200	Strong transcription	Liver	Liver
40	chr1:186374800-186383400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:186374800-186390800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:186375000-186383400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:186375600-186389800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr1:186376200-186388200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr1:186376600-186387800	Weak transcription	Brain Anterior Caudate	brain
46	chr1:186376800-186388000	Weak transcription	Fetal Brain Female	brain
47	chr1:186376800-186391800	Weak transcription	HepG2	liver
48	chr1:186376800-186399600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:186377000-186388000	Weak transcription	Primary T cells from cord blood	blood
50	chr1:186377200-186388000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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