Variant report

Variant	rs11957827
Chromosome Location	chr5:58297408-58297409
allele	C/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	chr5:58297043-58297894	PFSK-1	brain:	n/a	n/a
2	TCF12	chr5:58296869-58297458	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr5:58296937-58298616	A549	lung:	n/a	n/a
4	MXI1	chr5:58296790-58297964	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr5:58297173-58297566	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
PDE4D	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10052704	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10053177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10061320	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10063703	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10065498	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10065540	0.82[AFR][1000 genomes]
rs10067196	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10069187	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10223103	0.82[AFR][1000 genomes]
rs10940638	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];1.00[ASN][1000 genomes]
rs11750426	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];1.00[ASN][1000 genomes]
rs11948356	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13357540	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13361043	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13362239	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13362296	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16888990	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];1.00[ASN][1000 genomes]
rs16888998	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];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1874857	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1874858	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1874859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2055296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055298	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];1.00[ASN][1000 genomes]
rs2291851	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2291852	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4279300	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4469166	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4631140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4699932	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];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4700315	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];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4700316	0.83[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4700317	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57527145	0.82[AFR][1000 genomes]
rs58779089	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58940834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61511922	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62358484	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62358490	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62358491	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62358492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6450498	0.83[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs6876057	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];0.95[ASN][1000 genomes]
rs6888474	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7714489	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7723432	0.86[CHB][hapmap];0.94[YRI][hapmap]
rs7727206	0.86[CHB][hapmap];0.94[YRI][hapmap]
rs7729722	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7733884	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7735570	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9283720	0.83[CHB][hapmap];0.94[YRI][hapmap]
rs9292184	0.86[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9292186	0.83[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9292187	0.83[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9292188	0.83[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs9292189	0.83[CHB][hapmap];0.94[YRI][hapmap]

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:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58278400-58299000	Weak transcription	Gastric	stomach
2	chr5:58279200-58314000	Weak transcription	Primary B cells from cord blood	blood
3	chr5:58279400-58317600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:58279600-58330400	Weak transcription	Fetal Stomach	stomach
5	chr5:58279800-58298200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:58280200-58299400	Weak transcription	Right Ventricle	heart
7	chr5:58280400-58297600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:58281800-58321600	Weak transcription	Osteobl	bone
9	chr5:58282400-58306600	Weak transcription	Fetal Intestine Small	intestine
10	chr5:58284400-58297600	Weak transcription	Fetal Lung	lung
11	chr5:58284400-58299200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr5:58286200-58298400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr5:58286200-58312800	Weak transcription	Lung	lung
14	chr5:58286200-58316200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr5:58286200-58330400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr5:58286200-58330600	Weak transcription	Thymus	Thymus
17	chr5:58286600-58298200	Weak transcription	Left Ventricle	heart
18	chr5:58286800-58312200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:58286800-58312600	Weak transcription	Fetal Thymus	thymus
20	chr5:58286800-58312800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr5:58287000-58298200	Weak transcription	Fetal Muscle Leg	muscle
22	chr5:58287200-58298400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr5:58287400-58301600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr5:58288800-58297600	Weak transcription	HSMM	muscle
25	chr5:58288800-58330600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:58289400-58301800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr5:58289600-58301600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr5:58290200-58299000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr5:58293400-58305200	Enhancers	Primary T cells from cord blood	blood
30	chr5:58293600-58297600	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr5:58293800-58297600	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr5:58294800-58299800	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr5:58295400-58303200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr5:58295600-58297600	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr5:58295600-58299000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr5:58296000-58300800	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr5:58296000-58312400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr5:58296000-58321600	Weak transcription	Aorta	Aorta
39	chr5:58296200-58297800	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr5:58296200-58298000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr5:58296200-58302800	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr5:58296400-58297600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:58296400-58297800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr5:58296400-58297800	Genic enhancers	A549	lung
45	chr5:58296400-58298200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr5:58296400-58298200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr5:58296400-58298200	Weak transcription	Small Intestine	intestine
48	chr5:58296400-58298400	Weak transcription	Brain Anterior Caudate	brain
49	chr5:58296400-58298400	Weak transcription	Brain Cingulate Gyrus	brain
50	chr5:58296400-58298400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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