Variant report

Variant	rs16841229
Chromosome Location	chr4:7784368-7784369
allele	G/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	ATF2	chr4:7784271-7784966	GM12878	blood:	n/a	n/a
2	FOXM1	chr4:7784335-7784957	GM12878	blood:	n/a	n/a
3	MEF2A	chr4:7784332-7785002	GM12878	blood:	n/a	chr4:7784555-7784569 chr4:7784569-7784584 chr4:7784710-7784718 chr4:7784568-7784583 chr4:7784364-7784379 chr4:7784571-7784580 chr4:7784564-7784585 chr4:7784486-7784500 chr4:7784570-7784581 chr4:7784488-7784497 chr4:7784564-7784585 chr4:7784481-7784502 chr4:7784487-7784498 chr4:7784569-7784583
4	ATF2	chr4:7784335-7784943	GM12878	blood:	n/a	n/a
5	BCLAF1	chr4:7784344-7784944	GM12878	blood:	n/a	n/a
6	MEF2C	chr4:7784295-7784885	GM12878	blood:	n/a	chr4:7784555-7784569 chr4:7784569-7784584 chr4:7784710-7784718 chr4:7784568-7784583 chr4:7784364-7784379 chr4:7784571-7784580 chr4:7784564-7784585 chr4:7784486-7784500 chr4:7784570-7784581 chr4:7784488-7784497 chr4:7784564-7784585 chr4:7784481-7784502 chr4:7784487-7784498 chr4:7784569-7784583 chr4:7784567-7784582
7	MTA3	chr4:7784275-7785004	GM12878	blood:	n/a	n/a
8	RUNX3	chr4:7784206-7784929	GM12878	blood:	n/a	n/a
9	NFIC	chr4:7784325-7784912	GM12878	blood:	n/a	n/a
10	NFIC	chr4:7784220-7785002	GM12878	blood:	n/a	n/a
11	MEF2A	chr4:7784259-7784954	GM12878	blood:	n/a	chr4:7784555-7784569 chr4:7784569-7784584 chr4:7784710-7784718 chr4:7784568-7784583 chr4:7784364-7784379 chr4:7784571-7784580 chr4:7784564-7784585 chr4:7784486-7784500 chr4:7784570-7784581 chr4:7784488-7784497 chr4:7784564-7784585 chr4:7784481-7784502 chr4:7784487-7784498 chr4:7784569-7784583

No.	Distal block	Cell Line	Cell type
1	chr4:7782182..7784812-chr4:7794360..7796536,2	K562	blood:
2	chr4:7765704..7768382-chr4:7782855..7784797,2	K562	blood:
3	chr4:7783261..7784863-chr4:7786642..7789248,2	K562	blood:

Variant related genes	Relation type
AFAP1	TF binding region
ENSG00000196526	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10015031	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025154	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10032821	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12644614	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12645231	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1557817	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16841211	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2018399	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2107182	0.82[ASN][1000 genomes]
rs28460880	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28729246	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234829	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4689161	0.80[ASN][1000 genomes]
rs55689818	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60422709	0.93[EUR][1000 genomes]
rs6446619	0.86[ASN][1000 genomes]
rs6827395	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6828807	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6829473	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9790401	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9917925	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7758400-7795400	Weak transcription	Hela-S3	cervix
2	chr4:7759400-7790400	Weak transcription	Psoas Muscle	Psoas
3	chr4:7761400-7784400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:7762000-7788000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:7762000-7805800	Weak transcription	Stomach Mucosa	stomach
6	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr4:7776000-7784400	Strong transcription	Fetal Intestine Small	intestine
8	chr4:7776400-7787200	Weak transcription	Fetal Brain Male	brain
9	chr4:7776400-7790000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:7776400-7799000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr4:7776400-7800000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr4:7776400-7806800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:7776600-7785400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:7777000-7785800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:7778000-7784400	Strong transcription	Fetal Brain Female	brain
16	chr4:7780200-7794400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:7780600-7785800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:7780600-7788000	Genic enhancers	Osteobl	bone
19	chr4:7780600-7800200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr4:7780800-7784800	Genic enhancers	NH-A	brain
21	chr4:7780800-7790600	Weak transcription	Pancreas	Pancrea
22	chr4:7781000-7784400	Genic enhancers	Fetal Stomach	stomach
23	chr4:7781000-7800000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr4:7781200-7796000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr4:7781400-7784800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:7781400-7786000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr4:7781400-7800400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr4:7781400-7801000	Weak transcription	Brain Substantia Nigra	brain
29	chr4:7781400-7801200	Weak transcription	Brain Anterior Caudate	brain
30	chr4:7781600-7784600	Weak transcription	A549	lung
31	chr4:7781600-7786000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr4:7781600-7786800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr4:7781600-7789400	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr4:7781600-7791400	Strong transcription	Fetal Intestine Large	intestine
35	chr4:7781600-7807400	Weak transcription	Brain Angular Gyrus	brain
36	chr4:7781800-7786800	Weak transcription	Fetal Kidney	kidney
37	chr4:7781800-7790000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:7782000-7786000	Enhancers	Fetal Heart	heart
39	chr4:7782000-7786600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:7782000-7790600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr4:7782200-7785400	Enhancers	Rectal Smooth Muscle	rectum
42	chr4:7782200-7791000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr4:7782400-7784800	Enhancers	Colon Smooth Muscle	Colon
44	chr4:7782600-7790800	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr4:7782800-7784400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr4:7782800-7784800	Genic enhancers	Fetal Lung	lung
47	chr4:7782800-7785800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr4:7782800-7785800	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr4:7783000-7784400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr4:7783000-7784400	Enhancers	Duodenum Smooth Muscle	Duodenum

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