Variant report

Variant	rs68141011
Chromosome Location	chr6:28217797-28217798
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28217166..28222171-chr6:28233596..28237356,7	MCF-7	breast:
2	chr6:28107426..28110018-chr6:28217244..28218841,2	MCF-7	breast:
3	chr6:28217257..28219975-chr6:28319678..28321725,2	K562	blood:
4	chr6:28191711..28195552-chr6:28216768..28221883,5	MCF-7	breast:
5	chr6:28207533..28210874-chr6:28216267..28219988,4	MCF-7	breast:
6	chr6:28104411..28106188-chr6:28216933..28220029,3	MCF-7	breast:
7	chr6:28217084..28219662-chr6:28271676..28274035,2	K562	blood:

Variant related genes	Relation type
ENSG00000137185	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000198315	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10456362	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1076639	0.81[ASN][1000 genomes]
rs11755032	0.90[ASN][1000 genomes]
rs11965538	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13200462	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339899	0.88[ASN][1000 genomes]
rs1419183	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1679709	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679732	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778507	0.93[ASN][1000 genomes]
rs1778508	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778511	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1936365	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2743554	0.96[ASN][1000 genomes]
rs2743555	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2799077	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2799079	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61127718	0.80[ASN][1000 genomes]
rs6905391	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6920512	0.91[ASN][1000 genomes]
rs735765	0.92[EUR][1000 genomes]
rs7740487	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs853676	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853678	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853679	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853681	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853682	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs853685	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853687	0.81[ASN][1000 genomes]
rs853688	0.87[ASN][1000 genomes]
rs853694	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9366717	0.81[EUR][1000 genomes]
rs9368561	0.80[EUR][1000 genomes]
rs9393908	0.81[EUR][1000 genomes]
rs9461446	0.93[ASN][1000 genomes]
rs9461448	0.90[ASN][1000 genomes]
rs9461449	0.90[ASN][1000 genomes]
rs9468321	0.93[ASN][1000 genomes]
rs9468322	0.93[ASN][1000 genomes]
rs9468342	0.81[ASN][1000 genomes]
rs9986596	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs68141011	RP5-874C20.3	cis	Thyroid	GTEx
rs68141011	AL022393.7	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28193800-28218400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:28193800-28218400	Weak transcription	Stomach Mucosa	stomach
3	chr6:28201600-28219400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:28203000-28218400	Weak transcription	HUVEC	blood vessel
5	chr6:28211600-28217800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:28211600-28218000	Strong transcription	Fetal Muscle Leg	muscle
7	chr6:28211800-28217800	Strong transcription	Fetal Thymus	thymus
8	chr6:28212000-28217800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:28212000-28217800	Strong transcription	Brain Substantia Nigra	brain
10	chr6:28212200-28217800	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:28212600-28217800	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:28212800-28218400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr6:28213600-28218000	Weak transcription	Pancreas	Pancrea
14	chr6:28213600-28218400	Weak transcription	Fetal Heart	heart
15	chr6:28213600-28218400	Weak transcription	NHEK	skin
16	chr6:28213800-28218200	Weak transcription	HMEC	breast
17	chr6:28214000-28218400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:28214200-28218400	Weak transcription	Small Intestine	intestine
19	chr6:28214200-28218400	Weak transcription	Hela-S3	cervix
20	chr6:28214400-28218400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr6:28214400-28219200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:28214600-28218000	Weak transcription	Psoas Muscle	Psoas
23	chr6:28214600-28218600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr6:28214600-28219200	Weak transcription	Gastric	stomach
25	chr6:28214600-28219400	Weak transcription	Aorta	Aorta
26	chr6:28214800-28218400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr6:28214800-28218400	Weak transcription	Spleen	Spleen
28	chr6:28214800-28218400	Weak transcription	A549	lung
29	chr6:28214800-28218400	Weak transcription	NHDF-Ad	bronchial
30	chr6:28215000-28218000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:28215000-28218200	Weak transcription	Fetal Kidney	kidney
32	chr6:28215000-28218400	Weak transcription	HSMM	muscle
33	chr6:28215000-28218400	Weak transcription	Osteobl	bone
34	chr6:28215000-28218600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr6:28215000-28218600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:28215000-28218600	Weak transcription	Colonic Mucosa	Colon
37	chr6:28215000-28218600	Weak transcription	Right Ventricle	heart
38	chr6:28215200-28218400	Weak transcription	K562	blood
39	chr6:28215400-28218400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:28215600-28218400	Weak transcription	Brain Angular Gyrus	brain
41	chr6:28215600-28218400	Weak transcription	Colon Smooth Muscle	Colon
42	chr6:28215600-28218400	Weak transcription	NH-A	brain
43	chr6:28215800-28218200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr6:28215800-28218600	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr6:28216000-28218400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr6:28216000-28218400	Weak transcription	Fetal Brain Female	brain
47	chr6:28216000-28219200	Weak transcription	Lung	lung
48	chr6:28216200-28217800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr6:28216200-28218200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr6:28216200-28218200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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