Variant report

Variant	rs9292188
Chromosome Location	chr5:58300353-58300354
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:58299129-58300359	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr5:58300349-58300366	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr5:58300239-58303153	A549	lung:	n/a	n/a

Variant related genes	Relation type
PDE4D	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10036287	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10053177	0.82[AFR][1000 genomes]
rs10053330	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10061320	0.81[AFR][1000 genomes]
rs10063703	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10065540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10223103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10940638	0.83[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs11750426	0.83[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs11957827	0.83[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs13362239	0.89[YRI][hapmap]
rs13362296	0.89[YRI][hapmap]
rs16888990	0.87[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs16888998	0.87[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1874857	0.82[AFR][1000 genomes]
rs1874858	0.87[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1874859	0.82[AFR][1000 genomes]
rs2055296	0.82[AFR][1000 genomes]
rs2055297	0.82[AFR][1000 genomes]
rs2055298	0.83[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2291851	0.83[CHB][hapmap]
rs4469166	0.87[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs4493634	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4631140	0.82[AFR][1000 genomes]
rs4699932	0.87[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4700315	0.87[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4700316	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4700317	0.83[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs57527145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58940834	0.82[AFR][1000 genomes]
rs62358490	0.81[AFR][1000 genomes]
rs62358491	0.82[AFR][1000 genomes]
rs62358492	0.82[AFR][1000 genomes]
rs6450498	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6876057	0.83[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7723432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7727206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7735570	0.83[CHB][hapmap];1.00[YRI][hapmap]
rs9283720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9292184	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9292186	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9292187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9292189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58279200-58314000	Weak transcription	Primary B cells from cord blood	blood
2	chr5:58279400-58317600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:58279600-58330400	Weak transcription	Fetal Stomach	stomach
4	chr5:58281800-58321600	Weak transcription	Osteobl	bone
5	chr5:58282400-58306600	Weak transcription	Fetal Intestine Small	intestine
6	chr5:58286200-58312800	Weak transcription	Lung	lung
7	chr5:58286200-58316200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr5:58286200-58330400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr5:58286200-58330600	Weak transcription	Thymus	Thymus
10	chr5:58286800-58312200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:58286800-58312600	Weak transcription	Fetal Thymus	thymus
12	chr5:58286800-58312800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr5:58287400-58301600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr5:58288800-58330600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr5:58289400-58301800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr5:58289600-58301600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:58293400-58305200	Enhancers	Primary T cells from cord blood	blood
18	chr5:58295400-58303200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:58296000-58300800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr5:58296000-58312400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr5:58296000-58321600	Weak transcription	Aorta	Aorta
22	chr5:58296200-58302800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr5:58296400-58301400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr5:58296600-58300600	Weak transcription	Brain Germinal Matrix	brain
25	chr5:58296600-58300800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr5:58297200-58300600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr5:58297200-58300800	Enhancers	Psoas Muscle	Psoas
28	chr5:58297600-58301600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr5:58297600-58302800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr5:58298200-58301000	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr5:58298200-58301400	Weak transcription	Hela-S3	cervix
32	chr5:58298400-58300400	Enhancers	Fetal Brain Male	brain
33	chr5:58298400-58312600	Weak transcription	Fetal Lung	lung
34	chr5:58298600-58300600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr5:58298600-58301600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:58298600-58317800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr5:58298800-58300600	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr5:58298800-58300800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr5:58299000-58300800	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr5:58299200-58301800	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr5:58299400-58302000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr5:58299600-58301000	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr5:58299600-58301600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr5:58299600-58301800	Weak transcription	Gastric	stomach
45	chr5:58299600-58312400	Weak transcription	HSMM	muscle
46	chr5:58299600-58316600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr5:58299800-58300600	Genic enhancers	A549	lung
48	chr5:58299800-58300800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:58299800-58301800	Weak transcription	Left Ventricle	heart
50	chr5:58299800-58301800	Weak transcription	Right Atrium	heart

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