Variant report

Variant	rs1650660
Chromosome Location	chr5:79963463-79963464
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:79959818..79962346-chr5:79962374..79963921,2	MCF-7	breast:
2	chr5:79949741..79953345-chr5:79963177..79965614,3	K562	blood:
3	chr5:79948482..79951173-chr5:79961260..79964699,4	MCF-7	breast:
4	chr5:79864951..79867602-chr5:79962481..79965182,3	MCF-7	breast:
5	chr5:79956607..79959193-chr5:79962502..79964568,2	MCF-7	breast:
6	chr5:79959827..79961745-chr5:79962101..79964799,2	K562	blood:
7	chr5:79956480..79958255-chr5:79962360..79963991,2	MCF-7	breast:
8	chr5:79949216..79952432-chr5:79962559..79966205,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000189127	Chromatin interaction
ENSG00000113318	Chromatin interaction
ENSG00000228716	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1238951	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1643656	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1650684	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1650687	0.91[EUR][1000 genomes]
rs1650690	0.87[EUR][1000 genomes]
rs1650716	0.81[AMR][1000 genomes]
rs1650723	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1677658	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1677697	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1677705	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6151616	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6151636	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs836789	0.85[EUR][1000 genomes]
rs836790	0.85[EUR][1000 genomes]
rs836791	0.89[EUR][1000 genomes]
rs836792	0.89[EUR][1000 genomes]
rs836803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv10710	chr5:79956446-79964949	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1650660	MSH3	cis	Whole Blood	GTEx
rs1650660	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs1650660	MSH3	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79951600-79963600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:79951600-79969200	Weak transcription	Stomach Mucosa	stomach
3	chr5:79951600-79972200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:79951600-80015600	Weak transcription	Small Intestine	intestine
5	chr5:79951800-79964000	Weak transcription	Brain Substantia Nigra	brain
6	chr5:79951800-79982800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr5:79952000-79963800	Weak transcription	Fetal Heart	heart
8	chr5:79952200-79964200	Weak transcription	Brain Angular Gyrus	brain
9	chr5:79952200-79964200	Strong transcription	Fetal Muscle Trunk	muscle
10	chr5:79952200-79964200	Weak transcription	NHLF	lung
11	chr5:79952200-79975400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr5:79952400-79965000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr5:79952400-79967400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr5:79952400-79975400	Weak transcription	HSMMtube	muscle
15	chr5:79952400-79976600	Strong transcription	Fetal Thymus	thymus
16	chr5:79952400-79976800	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr5:79952400-79983000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:79952600-79963800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr5:79952600-79965000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:79952600-79985200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr5:79952600-79991600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr5:79952800-79972200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr5:79953000-79966400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr5:79953200-79963800	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr5:79953200-79964200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr5:79953200-79964200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:79953200-79965200	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr5:79953200-79980800	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr5:79953600-79964200	Strong transcription	Dnd41	blood
30	chr5:79953800-79969800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr5:79955200-79964400	Strong transcription	Primary hematopoietic stem cells	blood
32	chr5:79955400-79968800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:79955800-79964400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr5:79956200-79979000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:79956400-80015600	Weak transcription	Psoas Muscle	Psoas
36	chr5:79957000-79964200	Weak transcription	Left Ventricle	heart
37	chr5:79957600-79964400	Strong transcription	Fetal Lung	lung
38	chr5:79957600-79964600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr5:79957800-79964800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr5:79958200-79968800	Weak transcription	Brain Anterior Caudate	brain
41	chr5:79958200-79971600	Strong transcription	Fetal Muscle Leg	muscle
42	chr5:79958200-79998000	Weak transcription	Fetal Brain Male	brain
43	chr5:79958800-79969800	Strong transcription	Primary T cells from cord blood	blood
44	chr5:79959000-79964000	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr5:79959200-79964800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr5:79959400-79965200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr5:79959600-79963800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:79959800-79963600	Strong transcription	GM12878-XiMat	blood
49	chr5:79959800-79964200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr5:79959800-79964600	Strong transcription	Stomach Smooth Muscle	stomach

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