Variant report

Variant	rs2299031
Chromosome Location	chr6:28196718-28196719
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28186179..28187868-chr6:28196077..28199044,2	MCF-7	breast:
2	chr6:28107272..28109222-chr6:28196565..28198817,2	K562	blood:
3	chr6:28195857..28199662-chr6:28302729..28304554,3	K562	blood:
4	chr6:28191609..28196785-chr6:28301378..28305522,8	K562	blood:

Variant related genes	Relation type
ENSG00000176933	Chromatin interaction
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1150683	0.93[GIH][hapmap];0.82[MEX][hapmap]
rs11756111	1.00[JPT][hapmap]
rs11758148	1.00[JPT][hapmap]
rs11758337	1.00[JPT][hapmap]
rs11970439	1.00[JPT][hapmap]
rs1225709	0.81[GIH][hapmap];0.82[MEX][hapmap]
rs1474589	1.00[JPT][hapmap]
rs16893937	1.00[JPT][hapmap]
rs17301128	1.00[JPT][hapmap]
rs17776284	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871695	0.82[MEX][hapmap];0.87[TSI][hapmap]
rs203885	0.82[MEX][hapmap]
rs2185955	1.00[JPT][hapmap]
rs2235358	1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2235359	1.00[JPT][hapmap]
rs3800326	1.00[JPT][hapmap];1.00[MKK][hapmap];0.83[AMR][1000 genomes]
rs539474	0.82[MEX][hapmap]
rs6903652	1.00[JPT][hapmap]
rs6903823	0.88[JPT][hapmap]
rs6912584	1.00[JPT][hapmap]
rs6921919	1.00[JPT][hapmap]
rs6922111	1.00[JPT][hapmap]
rs73740569	0.80[AFR][1000 genomes]
rs73740570	0.80[AFR][1000 genomes]
rs73742509	0.89[ASN][1000 genomes]
rs7769054	1.00[JPT][hapmap]
rs9348795	0.82[MEX][hapmap]
rs9393905	0.86[AFR][1000 genomes]
rs993619	1.00[JPT][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	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

No data

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	chr6:28194800-28196800	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr6:28194800-28197200	Strong transcription	Placenta Amnion	Placenta Amnion
15	chr6:28194800-28199000	Strong transcription	HSMMtube	muscle
16	chr6:28194800-28202800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr6:28194800-28202800	Strong transcription	Fetal Muscle Trunk	muscle
18	chr6:28194800-28202800	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr6:28194800-28204200	Strong transcription	Left Ventricle	heart
20	chr6:28194800-28205000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:28195000-28196800	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr6:28195000-28196800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:28195000-28196800	Strong transcription	Brain Substantia Nigra	brain
24	chr6:28195000-28196800	Strong transcription	Pancreas	Pancrea
25	chr6:28195000-28197200	Strong transcription	Fetal Heart	heart
26	chr6:28195000-28197400	Strong transcription	Brain Hippocampus Middle	brain
27	chr6:28195000-28197400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:28195000-28198800	Strong transcription	Hela-S3	cervix
29	chr6:28195000-28199000	Strong transcription	HSMM	muscle
30	chr6:28195000-28199000	Strong transcription	Osteobl	bone
31	chr6:28195000-28199400	Strong transcription	Primary hematopoietic stem cells	blood
32	chr6:28195000-28199400	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr6:28195000-28199600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:28195000-28200000	Strong transcription	NH-A	brain
35	chr6:28195000-28200200	Strong transcription	HUVEC	blood vessel
36	chr6:28195000-28201200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:28195000-28201200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:28195000-28201200	Strong transcription	Ovary	ovary
39	chr6:28195000-28201400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:28195000-28201600	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr6:28195000-28201600	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr6:28195000-28201600	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr6:28195000-28201600	Strong transcription	HepG2	liver
44	chr6:28195000-28202000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr6:28195000-28202000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:28195000-28202000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:28195000-28202000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:28195000-28202000	Strong transcription	Stomach Smooth Muscle	stomach
49	chr6:28195000-28202200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:28195000-28202200	Strong transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links