Variant report

Variant	rs16825329
Chromosome Location	chr1:186386524-186386525
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:186384905..186386985-chr1:186417327..186419013,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRG4-2	chr1:186386509-186386786	NONHSAT008448

Variant related genes	Relation type
ENSG00000116703	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]
rs10494588	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[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]
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:120 , 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	chr1:186372000-186389400	Weak transcription	Gastric	stomach
26	chr1:186372000-186391000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:186372000-186392000	Weak transcription	Esophagus	oesophagus
28	chr1:186372000-186398200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:186372000-186406000	Weak transcription	Pancreas	Pancrea
30	chr1:186374800-186390800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:186375600-186389800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr1:186376200-186388200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr1:186376600-186387800	Weak transcription	Brain Anterior Caudate	brain
34	chr1:186376800-186388000	Weak transcription	Fetal Brain Female	brain
35	chr1:186376800-186391800	Weak transcription	HepG2	liver
36	chr1:186376800-186399600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:186377000-186388000	Weak transcription	Primary T cells from cord blood	blood
38	chr1:186377200-186388000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:186377400-186388000	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:186377600-186387800	Weak transcription	HMEC	breast
41	chr1:186377800-186388000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:186378600-186387600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:186378800-186387800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr1:186378800-186388000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:186379000-186387400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:186379000-186387600	Weak transcription	Fetal Muscle Leg	muscle
47	chr1:186379000-186388000	Weak transcription	Left Ventricle	heart
48	chr1:186379000-186388000	Weak transcription	Thymus	Thymus
49	chr1:186379000-186388200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:186379200-186390000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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