Variant report

Variant	rs602921
Chromosome Location	chr15:59003934-59003935
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	chr15:59002723..59004883-chr15:59065189..59066915,2	K562	blood:
2	chr15:58994779..58996470-chr15:59002182..59005147,2	K562	blood:

Variant related genes	Relation type
ENSG00000199730	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11631244	1.00[CEU][hapmap]
rs11632492	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11638416	1.00[CEU][hapmap]
rs11639208	1.00[CEU][hapmap]
rs16940571	1.00[CEU][hapmap]
rs16940810	1.00[CEU][hapmap]
rs2555787	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2657126	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs347118	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs347119	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs347121	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs347122	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs384322	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs387005	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs390390	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs415403	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs424346	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs437549	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs625510	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6494025	1.00[CEU][hapmap]
rs73426525	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs73426541	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs793417	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58977200-59004400	Weak transcription	Ovary	ovary
2	chr15:58977200-59007800	Weak transcription	HepG2	liver
3	chr15:58977200-59039200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:58982400-59005000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr15:58982600-59008000	Weak transcription	Fetal Brain Male	brain
6	chr15:58983200-59016600	Weak transcription	Small Intestine	intestine
7	chr15:58985200-59005000	Weak transcription	HSMMtube	muscle
8	chr15:58986600-59016600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr15:58987400-59012000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:58987600-59005000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:58987600-59007800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr15:58989800-59016800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:58990000-59004800	Weak transcription	Pancreas	Pancrea
14	chr15:58990000-59005000	Weak transcription	Spleen	Spleen
15	chr15:58990000-59005200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:58990000-59023400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:58991600-59005200	Weak transcription	Brain Hippocampus Middle	brain
18	chr15:58991800-59005000	Weak transcription	Liver	Liver
19	chr15:58991800-59005000	Weak transcription	Fetal Kidney	kidney
20	chr15:58991800-59005000	Weak transcription	HMEC	breast
21	chr15:58991800-59012200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:58992000-59005000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr15:58992000-59009000	Weak transcription	Placenta	Placenta
24	chr15:58992000-59010800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:58992000-59015800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr15:58992000-59023000	Weak transcription	Esophagus	oesophagus
27	chr15:58992000-59023800	Weak transcription	Aorta	Aorta
28	chr15:58992200-59004400	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:58992200-59008600	Weak transcription	Fetal Lung	lung
30	chr15:58992400-59004600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr15:58992400-59005000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr15:58992400-59005200	Weak transcription	NHEK	skin
33	chr15:58992400-59005600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr15:58992400-59011600	Weak transcription	HUVEC	blood vessel
35	chr15:58992400-59012000	Weak transcription	Brain Anterior Caudate	brain
36	chr15:58992600-59005000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr15:58992600-59016600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr15:58992600-59021000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr15:58992800-59007200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr15:58992800-59008400	Weak transcription	A549	lung
41	chr15:58993200-59005000	Weak transcription	Thymus	Thymus
42	chr15:58993200-59010200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr15:58993200-59010800	Weak transcription	K562	blood
44	chr15:58993400-59010600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:58994000-59005000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr15:58994200-59005000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr15:58994400-59004800	Weak transcription	Fetal Intestine Large	intestine
48	chr15:58994400-59012400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr15:58994400-59016400	Weak transcription	Adipose Nuclei	Adipose
50	chr15:58994800-59007600	Weak transcription	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links