Variant report

Variant	rs9939324
Chromosome Location	chr16:58540593-58540594
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	chr16:58540591-58540719	K562	blood:	n/a	n/a
2	POLR2A	chr16:58540164-58542421	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr16:58540507-58541011	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr16:58540441-58541656	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr16:58540557-58542695	A549	lung:	n/a	n/a
6	POLR2A	chr16:58540575-58540914	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:58539398..58543065-chr16:58544089..58547171,4	MCF-7	breast:
2	chr16:58540526..58542196-chr16:58550973..58553674,2	K562	blood:

Variant related genes	Relation type
NDRG4	TF binding region
ENSG00000103037	Chromatin interaction
ENSG00000103034	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs13329892	1.00[EUR][1000 genomes]
rs13334745	1.00[EUR][1000 genomes]
rs13334922	1.00[EUR][1000 genomes]
rs13335464	1.00[EUR][1000 genomes]
rs13335851	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13335953	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13337650	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13339352	1.00[EUR][1000 genomes]
rs28394663	1.00[EUR][1000 genomes]
rs28468502	1.00[EUR][1000 genomes]
rs28472773	1.00[EUR][1000 genomes]
rs28530777	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28533067	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28613241	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28644182	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28744389	1.00[EUR][1000 genomes]
rs34698978	1.00[EUR][1000 genomes]
rs57335704	1.00[EUR][1000 genomes]
rs7186446	1.00[EUR][1000 genomes]
rs7193580	1.00[EUR][1000 genomes]
rs73558468	1.00[EUR][1000 genomes]
rs8048686	1.00[EUR][1000 genomes]
rs9746055	1.00[EUR][1000 genomes]
rs9923409	1.00[EUR][1000 genomes]
rs9924494	1.00[EUR][1000 genomes]
rs9926053	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9930277	1.00[EUR][1000 genomes]
rs9938192	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9938386	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9941013	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9941175	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532532	chr16:58116482-58611986	Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv528512	chr16:58513813-58549014	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a
3	esv1803007	chr16:58515901-58553164	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
4	nsv1058290	chr16:58521026-58546709	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
5	nsv527052	chr16:58521090-58542901	Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
6	nsv906742	chr16:58538556-58553164	Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:58534600-58544800	Weak transcription	HSMMtube	muscle
2	chr16:58535600-58541600	Weak transcription	Osteobl	bone
3	chr16:58535800-58544400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:58535800-58548200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr16:58535800-58548400	Weak transcription	Gastric	stomach
6	chr16:58535800-58548800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr16:58536000-58540600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr16:58536000-58543000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr16:58536000-58548600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr16:58536200-58543000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr16:58536200-58548400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr16:58536200-58548600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr16:58536200-58548800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr16:58537000-58540600	Weak transcription	Brain Hippocampus Middle	brain
15	chr16:58537000-58548400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr16:58537200-58540600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr16:58537200-58545200	Weak transcription	Pancreas	Pancrea
18	chr16:58537200-58545400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr16:58537200-58548200	Weak transcription	Fetal Brain Male	brain
20	chr16:58537400-58547600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr16:58537800-58545600	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr16:58538000-58548400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr16:58538200-58542400	Weak transcription	Fetal Intestine Small	intestine
24	chr16:58538400-58542600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr16:58538400-58542600	Weak transcription	Esophagus	oesophagus
26	chr16:58538400-58543000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr16:58538400-58545000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr16:58538600-58540600	Weak transcription	Brain Angular Gyrus	brain
29	chr16:58538600-58541800	Weak transcription	Fetal Muscle Leg	muscle
30	chr16:58538600-58542400	Weak transcription	Spleen	Spleen
31	chr16:58538600-58543000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr16:58538600-58548600	Weak transcription	Brain Substantia Nigra	brain
33	chr16:58539000-58541600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr16:58539800-58544000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr16:58539800-58544200	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr16:58540000-58545600	Strong transcription	Right Ventricle	heart
37	chr16:58540200-58541200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr16:58540200-58541800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr16:58540200-58543200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr16:58540200-58543600	Strong transcription	Brain Cingulate Gyrus	brain
41	chr16:58540200-58544800	Strong transcription	Left Ventricle	heart
42	chr16:58540200-58545200	Strong transcription	Lung	lung
43	chr16:58540200-58545400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr16:58540200-58545400	Strong transcription	Fetal Stomach	stomach
45	chr16:58540200-58545600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr16:58540200-58546000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr16:58540200-58546000	Strong transcription	Fetal Brain Female	brain
48	chr16:58540200-58546400	Strong transcription	Brain Germinal Matrix	brain
49	chr16:58540400-58545800	Strong transcription	Brain Anterior Caudate	brain

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