Variant report

Variant	rs6453083
Chromosome Location	chr5:74075358-74075359
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:74062787..74065047-chr5:74073990..74076959,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164346	Chromatin interaction
ENSG00000164347	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10515191	0.81[YRI][hapmap]
rs1164624	0.91[ASW][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.94[YRI][hapmap]
rs1164692	0.83[CEU][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs11743655	0.81[YRI][hapmap]
rs11746702	0.81[YRI][hapmap]
rs11948188	0.81[YRI][hapmap]
rs11955898	0.81[YRI][hapmap]
rs12516674	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs15694	0.84[YRI][hapmap]
rs16872346	0.81[YRI][hapmap]
rs6453077	0.85[YRI][hapmap]
rs6453084	0.81[YRI][hapmap]
rs6859014	0.81[YRI][hapmap]
rs6874609	0.81[YRI][hapmap]

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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6453083	GFM2	cis	cerebellum	SCAN
rs6453083	NSA2	cis	Adipose Subcutaneous	GTEx
rs6453083	GFM2	cis	parietal	SCAN
rs6453083	NSA2	cis	parietal	SCAN
rs6453083	NSA2	cis	lung	GTEx
rs6453083	NSA2	cis	lymphoblastoid	seeQTL
rs6453083	NSA2	cis	cerebellum	SCAN
rs6453083	NSA2	cis	Heart Left Ventricle	GTEx
rs6453083	NSA2	cis	Skin Sun Exposed Lower leg	GTEx
rs6453083	NSA2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74064000-74076000	Weak transcription	Esophagus	oesophagus
2	chr5:74064000-74077200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:74064000-74112400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:74064200-74076000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:74064200-74086000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr5:74064200-74102000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:74064400-74076600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr5:74064400-74079600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:74064400-74086600	Weak transcription	Fetal Heart	heart
10	chr5:74064400-74134600	Weak transcription	Fetal Brain Male	brain
11	chr5:74064600-74079400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:74064600-74079600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr5:74064800-74079400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr5:74064800-74079600	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:74064800-74080000	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr5:74064800-74080400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr5:74064800-74101200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr5:74065000-74077800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr5:74065000-74079600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr5:74065000-74081800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:74065200-74076200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr5:74065400-74076400	Strong transcription	GM12878-XiMat	blood
23	chr5:74065400-74077800	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr5:74066600-74112800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr5:74066800-74075600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:74069000-74079400	Strong transcription	HepG2	liver
27	chr5:74069000-74153000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:74069600-74076000	Weak transcription	K562	blood
29	chr5:74069600-74102600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr5:74069800-74086400	Weak transcription	Brain Angular Gyrus	brain
31	chr5:74069800-74097000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr5:74070000-74077400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr5:74070000-74086200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr5:74070000-74095000	Weak transcription	Fetal Kidney	kidney
35	chr5:74070000-74097000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr5:74070000-74111600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr5:74070400-74075400	Weak transcription	Psoas Muscle	Psoas
38	chr5:74070400-74082600	Weak transcription	Brain Substantia Nigra	brain
39	chr5:74071000-74086200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr5:74071400-74075800	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr5:74071400-74078200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr5:74071400-74078800	Weak transcription	Right Ventricle	heart
43	chr5:74071400-74085800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr5:74071400-74086400	Weak transcription	Aorta	Aorta
45	chr5:74071400-74095200	Weak transcription	Spleen	Spleen
46	chr5:74071600-74076200	Strong transcription	A549	lung
47	chr5:74071600-74079400	Strong transcription	Dnd41	blood
48	chr5:74071800-74077600	Weak transcription	NHLF	lung
49	chr5:74072000-74077600	Weak transcription	Fetal Muscle Leg	muscle
50	chr5:74072200-74076000	Weak transcription	Brain Anterior Caudate	brain

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