Variant report

Variant	rs9307478
Chromosome Location	chr4:120460662-120460663
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	chr4:120460634-120460780	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
PDE5A	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10003953	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10010097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10012406	1.00[AMR][1000 genomes]
rs10015714	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10015999	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10017842	1.00[AMR][1000 genomes]
rs10021318	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10023384	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10027735	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10028634	1.00[AMR][1000 genomes]
rs10029882	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10031328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10032392	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10213498	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10471013	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11098519	1.00[AMR][1000 genomes]
rs11098520	1.00[AMR][1000 genomes]
rs17292047	1.00[YRI][hapmap]
rs28380652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28399227	1.00[AMR][1000 genomes]
rs28405434	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28419430	1.00[AMR][1000 genomes]
rs28436005	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28450144	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28461667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28469881	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28470408	1.00[AMR][1000 genomes]
rs28535588	1.00[AMR][1000 genomes]
rs28576329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28590285	1.00[AMR][1000 genomes]
rs28615474	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28622207	1.00[AMR][1000 genomes]
rs28634062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28639494	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28639769	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28651206	1.00[AMR][1000 genomes]
rs28654414	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28665114	1.00[AMR][1000 genomes]
rs28669906	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28709577	1.00[AMR][1000 genomes]
rs28736368	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28864814	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28870820	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3872804	1.00[AMR][1000 genomes]
rs55905129	1.00[AMR][1000 genomes]
rs56191916	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57295141	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57516186	1.00[AMR][1000 genomes]
rs59116083	1.00[AMR][1000 genomes]
rs61729464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61823285	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72918555	1.00[AMR][1000 genomes]
rs72918590	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72918597	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72920607	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72920619	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72920685	1.00[AMR][1000 genomes]
rs9884290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9884542	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9993996	1.00[AMR][1000 genomes]
rs9996803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9997423	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9998244	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv427694	chr4:120250511-120501728	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv879843	chr4:120326323-120502461	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv879846	chr4:120341296-120491714	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv879845	chr4:120341296-120502461	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120376400-120471600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:120377600-120501200	Weak transcription	Pancreas	Pancrea
3	chr4:120420200-120485400	Weak transcription	Fetal Brain Male	brain
4	chr4:120434600-120474400	Weak transcription	Gastric	stomach
5	chr4:120434800-120464800	Weak transcription	Lung	lung
6	chr4:120435000-120473200	Weak transcription	Esophagus	oesophagus
7	chr4:120435000-120487600	Weak transcription	Colonic Mucosa	Colon
8	chr4:120436200-120473800	Weak transcription	Fetal Brain Female	brain
9	chr4:120436600-120471600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:120436800-120474000	Weak transcription	Thymus	Thymus
11	chr4:120437600-120474200	Weak transcription	Brain Substantia Nigra	brain
12	chr4:120437800-120479200	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:120438200-120484800	Weak transcription	Brain Anterior Caudate	brain
14	chr4:120439400-120474200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr4:120440000-120474000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr4:120440600-120478200	Weak transcription	Primary B cells from cord blood	blood
17	chr4:120441200-120476200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:120441600-120472600	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr4:120442200-120474200	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr4:120442800-120484600	Weak transcription	Psoas Muscle	Psoas
21	chr4:120447400-120484800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:120447600-120463200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr4:120448000-120484800	Weak transcription	Fetal Heart	heart
24	chr4:120448400-120465000	Weak transcription	HSMMtube	muscle
25	chr4:120449400-120473600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr4:120451600-120485200	Weak transcription	Brain Angular Gyrus	brain
27	chr4:120452800-120465400	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr4:120453800-120461200	Weak transcription	NHEK	skin
29	chr4:120455600-120483800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr4:120456200-120488800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr4:120456400-120464800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr4:120456400-120471600	Weak transcription	Dnd41	blood
33	chr4:120456400-120472400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:120456400-120473000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr4:120456400-120484400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr4:120456400-120484800	Weak transcription	Liver	Liver
37	chr4:120456600-120462200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:120456600-120462200	Weak transcription	Fetal Muscle Leg	muscle
39	chr4:120456600-120464400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr4:120456600-120473800	Weak transcription	Fetal Thymus	thymus
41	chr4:120456600-120484600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr4:120456600-120484800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:120457800-120460800	Genic enhancers	NHLF	lung
44	chr4:120457800-120463800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:120457800-120463800	Weak transcription	HepG2	liver
46	chr4:120458200-120464200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr4:120458200-120472000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr4:120458200-120472200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr4:120458200-120484600	Weak transcription	Fetal Intestine Small	intestine
50	chr4:120458400-120461600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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