Variant report

Variant	rs668229
Chromosome Location	chr6:24928014-24928015
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1034159	1.00[EUR][1000 genomes]
rs1626799	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2149453	1.00[EUR][1000 genomes]
rs216263	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs422488	1.00[EUR][1000 genomes]
rs4712867	1.00[EUR][1000 genomes]
rs4712875	1.00[EUR][1000 genomes]
rs57596299	1.00[EUR][1000 genomes]
rs57969861	1.00[EUR][1000 genomes]
rs654491	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7742357	1.00[EUR][1000 genomes]
rs9467324	1.00[EUR][1000 genomes]
rs9467326	1.00[EUR][1000 genomes]
rs9467328	1.00[EUR][1000 genomes]
rs9467376	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1019504	chr6:24869174-24994758	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3422272	chr6:24925373-24929771	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv883482	chr6:24926730-25035920	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24919200-24930600	Weak transcription	Gastric	stomach
2	chr6:24919800-24928600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:24920600-24930000	Weak transcription	Right Atrium	heart
4	chr6:24920600-24932000	Weak transcription	Fetal Kidney	kidney
5	chr6:24921000-24928400	Weak transcription	Fetal Heart	heart
6	chr6:24921200-24929600	Weak transcription	Psoas Muscle	Psoas
7	chr6:24924400-24930000	Enhancers	Hela-S3	cervix
8	chr6:24924600-24929400	Weak transcription	Fetal Muscle Leg	muscle
9	chr6:24924600-24930600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:24924600-24930600	Weak transcription	Spleen	Spleen
11	chr6:24924600-24930800	Weak transcription	Brain Germinal Matrix	brain
12	chr6:24925000-24928400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:24925000-24930800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr6:24925400-24930600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr6:24925600-24930600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:24925600-24930600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr6:24925600-24931000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr6:24925600-24931000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr6:24925600-24931800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:24925800-24928200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:24926200-24928200	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:24926200-24930800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr6:24926400-24928400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
24	chr6:24926800-24928400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:24926800-24929400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
26	chr6:24926800-24931600	Weak transcription	Stomach Mucosa	stomach
27	chr6:24926800-24934400	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
28	chr6:24927000-24928200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:24927000-24928800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:24927000-24929600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:24927000-24930600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:24927000-24930600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr6:24927000-24930800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr6:24927000-24931600	Weak transcription	Fetal Intestine Small	intestine
35	chr6:24927200-24929400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr6:24927200-24929400	Weak transcription	Thymus	Thymus
37	chr6:24927200-24933600	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
38	chr6:24927400-24928200	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
39	chr6:24927400-24928200	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
40	chr6:24927400-24928600	Flanking Active TSS	GM12878-XiMat	blood
41	chr6:24927400-24929400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr6:24927400-24931800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:24927400-24932200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
44	chr6:24927600-24928200	Weak transcription	Fetal Thymus	thymus
45	chr6:24927600-24929200	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr6:24927600-24929600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:24927600-24931600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr6:24927600-24932400	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
49	chr6:24927800-24928200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:24927800-24928400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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