Variant report

Variant	rs2968015
Chromosome Location	chr5:58299169-58299170
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	chr5:58298882-58299845	A549	lung:	n/a	n/a
2	POLR2A	chr5:58299129-58300359	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr5:58299008-58299238	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
PDE4D	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10074854	0.93[EUR][1000 genomes]
rs10461657	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1463816	0.93[EUR][1000 genomes]
rs1498612	0.88[EUR][1000 genomes]
rs1532520	0.88[EUR][1000 genomes]
rs1553114	0.89[EUR][1000 genomes]
rs159724	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1846369	0.88[EUR][1000 genomes]
rs1973450	0.89[EUR][1000 genomes]
rs1973451	0.89[EUR][1000 genomes]
rs2409614	0.82[EUR][1000 genomes]
rs2927661	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2936190	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2936192	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2936193	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2936199	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2968006	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2968013	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968014	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2968017	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2968021	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3805553	0.93[EUR][1000 genomes]
rs3805554	0.91[EUR][1000 genomes]
rs3805556	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3805557	0.89[EUR][1000 genomes]
rs412423	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4321723	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs457959	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4621516	0.87[EUR][1000 genomes]
rs4629551	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4699930	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4699931	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4700314	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6450496	0.88[EUR][1000 genomes]
rs6875727	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs702519	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs702523	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7712725	0.87[EUR][1000 genomes]
rs7713069	0.88[EUR][1000 genomes]
rs7713345	0.88[EUR][1000 genomes]
rs7724713	0.93[EUR][1000 genomes]
rs7737685	0.92[EUR][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:75 , 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	chr5:58280200-58299400	Weak transcription	Right Ventricle	heart
5	chr5:58281800-58321600	Weak transcription	Osteobl	bone
6	chr5:58282400-58306600	Weak transcription	Fetal Intestine Small	intestine
7	chr5:58284400-58299200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr5:58286200-58312800	Weak transcription	Lung	lung
9	chr5:58286200-58316200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr5:58286200-58330400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr5:58286200-58330600	Weak transcription	Thymus	Thymus
12	chr5:58286800-58312200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:58286800-58312600	Weak transcription	Fetal Thymus	thymus
14	chr5:58286800-58312800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr5:58287400-58301600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr5:58288800-58330600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr5:58289400-58301800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr5:58289600-58301600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:58293400-58305200	Enhancers	Primary T cells from cord blood	blood
20	chr5:58294800-58299800	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr5:58295400-58303200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:58296000-58300800	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr5:58296000-58312400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr5:58296000-58321600	Weak transcription	Aorta	Aorta
25	chr5:58296200-58302800	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr5:58296400-58299200	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr5:58296400-58301400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr5:58296600-58300600	Weak transcription	Brain Germinal Matrix	brain
29	chr5:58296600-58300800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:58296800-58300000	Enhancers	Colon Smooth Muscle	Colon
31	chr5:58297000-58299800	Enhancers	Fetal Heart	heart
32	chr5:58297200-58300000	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr5:58297200-58300600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr5:58297200-58300800	Enhancers	Psoas Muscle	Psoas
35	chr5:58297400-58299200	Weak transcription	Fetal Brain Female	brain
36	chr5:58297400-58299600	Enhancers	HSMMtube	muscle
37	chr5:58297600-58299400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:58297600-58299600	Enhancers	Placenta Amnion	Placenta Amnion
39	chr5:58297600-58299800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:58297600-58301600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr5:58297600-58302800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr5:58298000-58299800	Enhancers	H1 Cell Line	embryonic stem cell
43	chr5:58298000-58300000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr5:58298000-58300200	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr5:58298200-58299800	Enhancers	H9 Cell Line	embryonic stem cell
46	chr5:58298200-58299800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr5:58298200-58299800	Enhancers	Fetal Muscle Leg	muscle
48	chr5:58298200-58299800	Enhancers	Left Ventricle	heart
49	chr5:58298200-58299800	Enhancers	Right Atrium	heart
50	chr5:58298200-58301000	Enhancers	HUES6 Cell Line	embryonic stem cell

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