Variant report

Variant	rs6870806
Chromosome Location	chr5:74067536-74067537
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:74062619..74065180-chr5:74065672..74068766,3	K562	blood:
2	chr5:74065827..74070020-chr5:74073603..74077107,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000199645	Chromatin interaction
ENSG00000164346	Chromatin interaction
ENSG00000164347	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1048167	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10515192	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10515194	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10515199	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739122	0.87[AFR][1000 genomes]
rs11742773	0.91[AFR][1000 genomes]
rs11749137	0.85[AFR][1000 genomes]
rs11959570	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1350097	0.88[AFR][1000 genomes]
rs16872220	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872231	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872235	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872242	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872259	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872323	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872345	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872347	0.80[AFR][1000 genomes]
rs16872349	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872362	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561738	1.00[ASN][1000 genomes]
rs2084116	0.91[AFR][1000 genomes]
rs2084118	0.91[AFR][1000 genomes]
rs2100033	0.91[AFR][1000 genomes]
rs3733794	0.93[AFR][1000 genomes]
rs55899032	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55920995	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56127814	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56192858	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56203772	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57202395	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57549677	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58864890	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60492282	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60663580	0.92[AFR][1000 genomes]
rs62366414	0.92[AFR][1000 genomes]
rs62366423	0.86[AFR][1000 genomes]
rs62366426	0.85[AFR][1000 genomes]
rs6453076	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6453079	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6453082	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6861935	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873912	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6873998	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6877188	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6877442	0.86[AFR][1000 genomes]
rs6881400	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6882035	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6882499	0.86[AFR][1000 genomes]
rs6883061	0.91[AFR][1000 genomes]
rs6883278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6883420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884338	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6884843	0.85[AFR][1000 genomes]
rs6885675	0.91[AFR][1000 genomes]
rs6894177	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6897698	0.85[AFR][1000 genomes]
rs6897904	0.85[AFR][1000 genomes]
rs6898684	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764630	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764643	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764647	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764648	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764650	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764654	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764655	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764656	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764657	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764663	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764669	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764675	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764676	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764683	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764684	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764687	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764690	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72766504	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7705519	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7713812	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7728889	0.80[AFR][1000 genomes]
rs7732440	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7732843	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs957680	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9686657	0.91[AFR][1000 genomes]
rs9765469	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598653	chr5:73992881-74095542	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers 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	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs6870806	NSA2	cis	lung	GTEx
rs6870806	NSA2	cis	Artery Tibial	GTEx
rs6870806	NSA2	cis	Thyroid	GTEx
rs6870806	NSA2	cis	Muscle Skeletal	GTEx
rs6870806	NSA2	cis	Nerve Tibial	GTEx
rs6870806	TINP1	Cis_1M	lymphoblastoid	RTeQTL
rs6870806	NSA2	cis	Heart Left Ventricle	GTEx
rs6870806	NSA2	cis	Adipose Subcutaneous	GTEx
rs6870806	NSA2	cis	Esophagus Mucosa	GTEx
rs6870806	NSA2	cis	Skin Sun Exposed Lower leg	GTEx
rs6870806	NSA2	cis	Stomach	GTEx
rs6870806	NSA2	cis	Whole Blood	GTEx
rs6870806	NSA2	cis	Artery Aorta	GTEx
rs6870806	NSA2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74063800-74069200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:74064000-74067800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:74064000-74068000	Weak transcription	Ovary	ovary
4	chr5:74064000-74068200	Weak transcription	Lung	lung
5	chr5:74064000-74070200	Weak transcription	Aorta	Aorta
6	chr5:74064000-74071000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:74064000-74076000	Weak transcription	Esophagus	oesophagus
8	chr5:74064000-74077200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:74064000-74112400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr5:74064200-74067600	Weak transcription	HSMMtube	muscle
11	chr5:74064200-74067800	Weak transcription	Psoas Muscle	Psoas
12	chr5:74064200-74068000	Weak transcription	Spleen	Spleen
13	chr5:74064200-74068200	Weak transcription	Primary B cells from cord blood	blood
14	chr5:74064200-74068200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:74064200-74068400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:74064200-74068400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr5:74064200-74068400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:74064200-74068600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr5:74064200-74069000	Weak transcription	Thymus	Thymus
20	chr5:74064200-74070600	Weak transcription	Pancreas	Pancrea
21	chr5:74064200-74073000	Weak transcription	Gastric	stomach
22	chr5:74064200-74073800	Weak transcription	Small Intestine	intestine
23	chr5:74064200-74076000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr5:74064200-74086000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr5:74064200-74102000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr5:74064400-74067800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:74064400-74068200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr5:74064400-74068400	Weak transcription	Colon Smooth Muscle	Colon
29	chr5:74064400-74068400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr5:74064400-74068400	Weak transcription	NHLF	lung
31	chr5:74064400-74068600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr5:74064400-74068600	Weak transcription	Brain Hippocampus Middle	brain
33	chr5:74064400-74073800	Weak transcription	Stomach Mucosa	stomach
34	chr5:74064400-74076600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr5:74064400-74079600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:74064400-74086600	Weak transcription	Fetal Heart	heart
37	chr5:74064400-74134600	Weak transcription	Fetal Brain Male	brain
38	chr5:74064600-74068000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr5:74064600-74068400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr5:74064600-74068400	Weak transcription	NHEK	skin
41	chr5:74064600-74074400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr5:74064600-74079400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:74064600-74079600	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr5:74064800-74067800	Strong transcription	Liver	Liver
45	chr5:74064800-74070000	Strong transcription	Dnd41	blood
46	chr5:74064800-74070000	Strong transcription	HMEC	breast
47	chr5:74064800-74072400	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr5:74064800-74074000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr5:74064800-74074400	Strong transcription	Osteobl	bone
50	chr5:74064800-74074600	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