Variant report

Variant	rs16890465
Chromosome Location	chr6:38204581-38204582
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10484933	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10947720	0.96[ASN][1000 genomes]
rs12524219	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs12529300	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs12529640	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16890468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16890511	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16890522	1.00[CHB][hapmap]
rs4711526	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4714135	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4714137	0.84[AMR][1000 genomes]
rs62397004	0.88[ASN][1000 genomes]
rs62397007	0.90[ASN][1000 genomes]
rs62397011	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62397015	0.87[AMR][1000 genomes]
rs6929505	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7739762	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv522522	chr6:38131442-38207636	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv520053	chr6:38154941-38207636	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38167000-38210400	Weak transcription	Primary T cells from cord blood	blood
2	chr6:38178000-38221600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr6:38178000-38221800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr6:38181000-38207600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:38181400-38229400	Weak transcription	Fetal Intestine Small	intestine
6	chr6:38186600-38215200	Weak transcription	Aorta	Aorta
7	chr6:38194400-38230200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:38198000-38204600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:38200000-38207600	Weak transcription	Lung	lung
10	chr6:38200600-38204800	Enhancers	H1 Cell Line	embryonic stem cell
11	chr6:38200600-38205200	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr6:38200600-38205200	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr6:38200600-38205400	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr6:38201600-38207200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:38202200-38207400	Weak transcription	Stomach Mucosa	stomach
16	chr6:38202200-38207600	Weak transcription	Gastric	stomach
17	chr6:38203200-38205400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:38203200-38205400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:38203400-38207800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:38203400-38212800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr6:38203800-38205200	Enhancers	GM12878-XiMat	blood
22	chr6:38203800-38207600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr6:38203800-38207800	Weak transcription	Psoas Muscle	Psoas
24	chr6:38203800-38207800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr6:38203800-38208000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:38204000-38207800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:38204000-38208800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr6:38204200-38215200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr6:38204400-38205000	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr6:38204400-38205000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:38204400-38205200	Enhancers	Cortex derived primary cultured neurospheres	brain

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