Variant report

Variant	rs16996151
Chromosome Location	chr4:89978800-89978801
allele	A/C
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	chr4:89977887-89978820	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr4:89977887-89978856	PFSK-1	brain:	n/a	n/a
3	USF1	chr4:89977859-89978819	HCT-116	colon:	n/a	chr4:89978378-89978387 chr4:89978375-89978386 chr4:89978377-89978386 chr4:89978377-89978386 chr4:89978371-89978392 chr4:89978376-89978385 chr4:89978375-89978388
4	RFX5	chr4:89978783-89978981	K562	blood:	n/a	n/a
5	POLR2A	chr4:89977672-89978822	MCF10A-Er-Src	breast:	n/a	n/a
6	KAP1	chr4:89978404-89979039	K562	blood:	n/a	n/a
7	MXI1	chr4:89977754-89978856	IMR90	lung:	n/a	n/a
8	IRF1	chr4:89976948-89978926	K562	blood:	n/a	chr4:89977624-89977637 chr4:89977623-89977637 chr4:89978870-89978880 chr4:89977626-89977636 chr4:89978508-89978521 chr4:89977626-89977640 chr4:89977622-89977636 chr4:89977624-89977637 chr4:89977624-89977638

No.	Distal block	Cell Line	Cell type
1	chr4:89743956..89746323-chr4:89976893..89978969,2	K562	blood:
2	chr4:89920516..89923501-chr4:89978516..89980046,2	K562	blood:
3	chr4:89977166..89979264-chr4:90032025..90033904,2	K562	blood:
4	chr4:89978596..89980145-chr4:89983083..89985851,2	K562	blood:

Variant related genes	Relation type
FAM13A	TF binding region
ENSG00000138640	Chromatin interaction
ENSG00000271359	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10516824	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs17014896	1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs17014898	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs17014901	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs17014931	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs17014934	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs17014939	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs17014952	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs17014954	1.00[AFR][1000 genomes]
rs17014962	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs17014966	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs17014977	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs17014983	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs17015012	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs56749689	1.00[AFR][1000 genomes]
rs60843670	1.00[AFR][1000 genomes]
rs61049728	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv461577	chr4:89904124-89986326	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv594807	chr4:89904124-89986326	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Response to antipsychotic therapy (extrapyramidal side effects)	19875103	GWAS catalog

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89975200-89979200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:89975600-89978800	Active TSS	Duodenum Mucosa	Duodenum
3	chr4:89975800-89978800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:89976000-89978800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr4:89976000-89978800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr4:89976000-89978800	Active TSS	Aorta	Aorta
7	chr4:89976000-89978800	Active TSS	Right Atrium	heart
8	chr4:89976200-89978800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr4:89976200-89978800	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr4:89976200-89978800	Active TSS	Ovary	ovary
11	chr4:89976400-89978800	Active TSS	HMEC	breast
12	chr4:89976600-89978800	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr4:89976600-89978800	Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr4:89976600-89978800	Flanking Active TSS	HUVEC	blood vessel
15	chr4:89976600-89979000	Active TSS	Stomach Smooth Muscle	stomach
16	chr4:89976600-89979000	Active TSS	K562	blood
17	chr4:89976800-89978800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:89976800-89978800	Active TSS	Fetal Kidney	kidney
19	chr4:89976800-89978800	Active TSS	Fetal Muscle Leg	muscle
20	chr4:89977000-89978800	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr4:89977000-89978800	Active TSS	Adipose Nuclei	Adipose
22	chr4:89977000-89978800	Active TSS	Brain Hippocampus Middle	brain
23	chr4:89977000-89978800	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr4:89977000-89978800	Active TSS	Fetal Brain Male	brain
25	chr4:89977000-89978800	Active TSS	Fetal Intestine Small	intestine
26	chr4:89977000-89978800	Active TSS	Fetal Muscle Trunk	muscle
27	chr4:89977000-89978800	Active TSS	Fetal Stomach	stomach
28	chr4:89977000-89978800	Active TSS	Psoas Muscle	Psoas
29	chr4:89977000-89978800	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr4:89977000-89978800	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr4:89977000-89978800	Active TSS	NHDF-Ad	bronchial
32	chr4:89977200-89978800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:89977200-89978800	Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr4:89977200-89978800	Active TSS	Colon Smooth Muscle	Colon
35	chr4:89977200-89978800	Active TSS	Fetal Brain Female	brain
36	chr4:89977200-89978800	Active TSS	Fetal Heart	heart
37	chr4:89977200-89978800	Active TSS	Fetal Intestine Large	intestine
38	chr4:89977200-89978800	Active TSS	NH-A	brain
39	chr4:89977400-89979000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:89977600-89978800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr4:89977600-89978800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:89977600-89978800	Active TSS	Brain Angular Gyrus	brain
43	chr4:89977600-89978800	Active TSS	Brain Anterior Caudate	brain
44	chr4:89977600-89978800	Active TSS	Brain Cingulate Gyrus	brain
45	chr4:89977600-89978800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr4:89977600-89978800	Active TSS	Fetal Thymus	thymus
47	chr4:89977600-89978800	Active TSS	Stomach Mucosa	stomach
48	chr4:89977800-89978800	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr4:89977800-89978800	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr4:89977800-89978800	Active TSS	Brain Substantia Nigra	brain

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