Variant report

Variant	rs6873176
Chromosome Location	chr5:36220958-36220959
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:36220947-36220966	A549	lung:	n/a	n/a
2	POLR2A	chr5:36220918-36220977	MCF-7	breast:	n/a	n/a

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

Variant related genes	Relation type
NADK2-AS1	TF binding region
NADK2	TF binding region
ENSG00000152620	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10051604	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10079844	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10079850	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10080095	0.91[ASN][1000 genomes]
rs10214173	0.91[ASN][1000 genomes]
rs10223062	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1035480	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10473001	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10473002	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10512643	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10737962	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10805609	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10805610	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10805611	0.91[ASN][1000 genomes]
rs10805612	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11747169	0.91[ASN][1000 genomes]
rs13360059	0.91[ASN][1000 genomes]
rs1345776	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1363843	0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1363844	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1364017	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1423223	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1423224	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1423226	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs152365	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs152366	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1816101	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1862543	0.91[ASN][1000 genomes]
rs1862544	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2303163	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2362978	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2362980	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2363034	0.81[CHB][hapmap]
rs27733	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs33663	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34888491	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3761974	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3849786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3860801	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3906394	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs41445147	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs430421	0.88[ASN][1000 genomes]
rs4869473	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4869474	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4869626	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4869634	0.91[ASN][1000 genomes]
rs4869635	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4869636	0.91[ASN][1000 genomes]
rs6451262	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6451263	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6451265	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6451269	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6451270	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6863707	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6866745	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6869599	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6870255	0.93[ASN][1000 genomes]
rs6874389	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs6881086	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6886098	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6891120	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6892199	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6893107	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6895423	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898215	0.90[ASN][1000 genomes]
rs7705209	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7705396	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7705858	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7705985	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7715317	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7720779	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7722251	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7724057	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7729152	0.83[ASN][1000 genomes]
rs878607	0.91[ASN][1000 genomes]
rs991032	0.91[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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	chr5:36211400-36221600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:36212400-36226800	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr5:36213200-36224800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:36213200-36225000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:36213200-36230200	Weak transcription	Brain Germinal Matrix	brain
34	chr5:36213200-36237000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr5:36213400-36227600	Weak transcription	NH-A	brain
36	chr5:36214400-36221200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr5:36214400-36222600	Strong transcription	Dnd41	blood
38	chr5:36214800-36221800	Strong transcription	Osteobl	bone
39	chr5:36214800-36222800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr5:36214800-36226200	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr5:36215200-36236600	Weak transcription	Small Intestine	intestine
42	chr5:36215600-36221600	Strong transcription	Primary hematopoietic stem cells	blood
43	chr5:36215800-36237800	Weak transcription	HMEC	breast
44	chr5:36216400-36223000	Weak transcription	Fetal Brain Female	brain
45	chr5:36216400-36225800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr5:36216800-36222600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr5:36216800-36228400	Weak transcription	HUVEC	blood vessel
48	chr5:36217600-36221000	Genic enhancers	Liver	Liver
49	chr5:36218800-36222200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr5:36219000-36221400	Strong transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links