Variant report

Variant	rs16902827
Chromosome Location	chr5:36221748-36221749
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:36220213..36223106-chr5:36238566..36243203,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SKP2-1	chr5:36221640-36222004	ENSG00000245711.2

Variant related genes	Relation type
ENSG00000152620	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10461961	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10461962	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10461964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10461965	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10512642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10512648	1.00[AFR][1000 genomes]
rs10941282	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10941283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10941284	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12054662	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12054682	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12054958	1.00[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12055219	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12652746	1.00[AFR][1000 genomes]
rs12654720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12655033	1.00[ASW][hapmap];1.00[AFR][1000 genomes]
rs12656102	0.87[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12657110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12658779	0.87[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1364013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1364014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1364015	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16902793	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16902797	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16902801	1.00[AFR][1000 genomes]
rs16902812	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16902813	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16902836	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16902845	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16902871	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16902911	0.86[CHB][hapmap];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs16902928	0.89[MEX][hapmap]
rs2202006	0.89[MEX][hapmap]
rs28362652	1.00[AFR][1000 genomes]
rs2937535	1.00[AFR][1000 genomes]
rs3849785	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3849787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3900936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4869470	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4869471	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4869472	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4869624	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4869627	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4869628	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4869629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4869630	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4869633	0.85[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4869637	1.00[ASW][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs56815690	0.86[ASN][1000 genomes]
rs59754678	0.84[ASN][1000 genomes]
rs6886540	0.87[CHB][hapmap];0.91[CHD][hapmap];0.82[ASN][1000 genomes]
rs6898451	0.84[ASN][1000 genomes]
rs73081933	0.86[ASN][1000 genomes]
rs878608	0.87[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9637790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs991033	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs991034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830262	chr5:36074311-36293872	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats 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	63 gene(s)	inside rSNPs	diseases
2	nsv1015638	chr5:36203646-36312576	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36172000-36229200	Weak transcription	Colonic Mucosa	Colon
2	chr5:36175600-36222400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:36179000-36222800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:36179000-36230000	Weak transcription	Psoas Muscle	Psoas
5	chr5:36190600-36227400	Weak transcription	Thymus	Thymus
6	chr5:36191800-36230000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:36192000-36224200	Weak transcription	Aorta	Aorta
8	chr5:36192600-36227800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr5:36196600-36236600	Weak transcription	GM12878-XiMat	blood
10	chr5:36197800-36224800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:36198000-36238400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:36200000-36229600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr5:36200200-36239400	Weak transcription	Fetal Brain Male	brain
14	chr5:36201200-36222000	Weak transcription	A549	lung
15	chr5:36201200-36230200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr5:36201400-36240000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr5:36203800-36227000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:36204000-36222600	Weak transcription	Fetal Heart	heart
19	chr5:36204000-36227000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:36205200-36226800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:36205800-36221800	Weak transcription	Colon Smooth Muscle	Colon
22	chr5:36209000-36222800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:36210400-36223000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:36210400-36223200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr5:36210600-36222000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr5:36210600-36222600	Weak transcription	NHLF	lung
27	chr5:36210600-36225000	Weak transcription	NHEK	skin
28	chr5:36210600-36225200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr5:36212400-36226800	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr5:36213200-36224800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr5:36213200-36225000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr5:36213200-36230200	Weak transcription	Brain Germinal Matrix	brain
33	chr5:36213200-36237000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr5:36213400-36227600	Weak transcription	NH-A	brain
35	chr5:36214400-36222600	Strong transcription	Dnd41	blood
36	chr5:36214800-36221800	Strong transcription	Osteobl	bone
37	chr5:36214800-36222800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:36214800-36226200	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr5:36215200-36236600	Weak transcription	Small Intestine	intestine
40	chr5:36215800-36237800	Weak transcription	HMEC	breast
41	chr5:36216400-36223000	Weak transcription	Fetal Brain Female	brain
42	chr5:36216400-36225800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr5:36216800-36222600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr5:36216800-36228400	Weak transcription	HUVEC	blood vessel
45	chr5:36218800-36222200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr5:36219000-36222200	Strong transcription	Fetal Intestine Large	intestine
47	chr5:36219000-36226600	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr5:36219000-36227000	Strong transcription	HepG2	liver
49	chr5:36219200-36221800	Strong transcription	Duodenum Mucosa	Duodenum
50	chr5:36219200-36226600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links