Variant report

Variant	rs2299029
Chromosome Location	chr6:28198831-28198832
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28109641..28111388-chr6:28197093..28199028,2	K562	blood:
2	chr6:28197985..28199991-chr6:28239613..28241567,2	K562	blood:
3	chr6:28186179..28187868-chr6:28196077..28199044,2	MCF-7	breast:
4	chr6:28198039..28200844-chr6:28211243..28213952,3	MCF-7	breast:
5	chr6:28195857..28199662-chr6:28302729..28304554,3	K562	blood:
6	chr6:28198177..28200363-chr6:28214686..28217029,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197062	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000198315	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11962305	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11967137	0.99[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1736904	0.89[EUR][1000 genomes]
rs34477097	0.94[AFR][1000 genomes]
rs34787248	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9295768	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9357067	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9366718	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs9368563	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9393909	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9393910	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461443	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9468317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9468318	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs967005	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2299029	AL022393.7	cis	Muscle Skeletal	GTEx
rs2299029	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs2299029	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28193600-28213400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:28193800-28204000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:28193800-28211800	Weak transcription	Fetal Thymus	thymus
4	chr6:28193800-28218400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:28193800-28218400	Weak transcription	Stomach Mucosa	stomach
6	chr6:28194000-28211000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr6:28194000-28211800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:28194000-28212800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:28194000-28213000	Weak transcription	Thymus	Thymus
10	chr6:28194000-28213600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr6:28194600-28199800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:28194600-28207000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:28194800-28199000	Strong transcription	HSMMtube	muscle
14	chr6:28194800-28202800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:28194800-28202800	Strong transcription	Fetal Muscle Trunk	muscle
16	chr6:28194800-28202800	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr6:28194800-28204200	Strong transcription	Left Ventricle	heart
18	chr6:28194800-28205000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:28195000-28199000	Strong transcription	HSMM	muscle
20	chr6:28195000-28199000	Strong transcription	Osteobl	bone
21	chr6:28195000-28199400	Strong transcription	Primary hematopoietic stem cells	blood
22	chr6:28195000-28199400	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr6:28195000-28199600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:28195000-28200000	Strong transcription	NH-A	brain
25	chr6:28195000-28200200	Strong transcription	HUVEC	blood vessel
26	chr6:28195000-28201200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:28195000-28201200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:28195000-28201200	Strong transcription	Ovary	ovary
29	chr6:28195000-28201400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:28195000-28201600	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr6:28195000-28201600	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr6:28195000-28201600	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:28195000-28201600	Strong transcription	HepG2	liver
34	chr6:28195000-28202000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr6:28195000-28202000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:28195000-28202000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:28195000-28202000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:28195000-28202000	Strong transcription	Stomach Smooth Muscle	stomach
39	chr6:28195000-28202200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:28195000-28202200	Strong transcription	Duodenum Mucosa	Duodenum
41	chr6:28195000-28202200	Strong transcription	Fetal Lung	lung
42	chr6:28195000-28202400	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr6:28195000-28202600	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr6:28195000-28202600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr6:28195000-28202600	Strong transcription	Fetal Stomach	stomach
46	chr6:28195000-28202600	Strong transcription	NHLF	lung
47	chr6:28195000-28202800	Strong transcription	Liver	Liver
48	chr6:28195000-28203000	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr6:28195000-28203000	Strong transcription	Fetal Intestine Large	intestine
50	chr6:28195000-28203200	Strong transcription	HUES64 Cell Line	embryonic stem cell

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