Variant report

Variant	rs16998546
Chromosome Location	chr4:143237243-143237244
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	chr4:143237041-143237664	H1-neurons	neurons:	n/a	n/a
2	REST	chr4:143236944-143237781	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr4:143237080-143237593	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:143232269..143234234-chr4:143236195..143238233,2	K562	blood:

Variant related genes	Relation type
LSM3P4	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10519654	1.00[AMR][1000 genomes]
rs10519658	1.00[AMR][1000 genomes]
rs1489579	1.00[AMR][1000 genomes]
rs17016047	1.00[AMR][1000 genomes]
rs17016073	1.00[AMR][1000 genomes]
rs17016097	1.00[AMR][1000 genomes]
rs28361347	1.00[AMR][1000 genomes]
rs28552507	1.00[AMR][1000 genomes]
rs55734648	1.00[AMR][1000 genomes]
rs55924247	1.00[AMR][1000 genomes]
rs58466279	1.00[AMR][1000 genomes]
rs59339281	1.00[AMR][1000 genomes]
rs60408738	1.00[AMR][1000 genomes]
rs61368063	1.00[AMR][1000 genomes]
rs61643803	1.00[AMR][1000 genomes]
rs6845221	1.00[AMR][1000 genomes]
rs72941201	1.00[AMR][1000 genomes]
rs72944962	1.00[AMR][1000 genomes]
rs72944976	1.00[AMR][1000 genomes]
rs9654254	0.87[YRI][hapmap];0.80[AFR][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	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1027781	chr4:142943485-143306567	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830099	chr4:143138257-143285055	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv830100	chr4:143216951-143393305	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143200000-143240000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:143217600-143238600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:143217600-143260800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:143223600-143239200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:143225400-143237400	Weak transcription	Ovary	ovary
6	chr4:143225400-143240200	Weak transcription	Esophagus	oesophagus
7	chr4:143231400-143239400	Weak transcription	HSMMtube	muscle
8	chr4:143233800-143241000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
9	chr4:143233800-143257200	Weak transcription	Left Ventricle	heart
10	chr4:143234000-143242000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:143234200-143240000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:143234600-143237400	Enhancers	Small Intestine	intestine
13	chr4:143234600-143237600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr4:143234800-143271800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr4:143235000-143237400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:143235000-143240000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr4:143235000-143240200	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr4:143235000-143243200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr4:143235000-143244200	Weak transcription	NHDF-Ad	bronchial
20	chr4:143235600-143238200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:143235600-143238600	Weak transcription	Psoas Muscle	Psoas
22	chr4:143235600-143266400	Weak transcription	NHEK	skin
23	chr4:143235800-143237600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr4:143235800-143239400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr4:143235800-143241600	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr4:143236000-143237600	Enhancers	Duodenum Mucosa	Duodenum
27	chr4:143236000-143237600	Enhancers	Fetal Intestine Large	intestine
28	chr4:143236000-143237600	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr4:143236000-143237600	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr4:143236000-143239600	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr4:143236000-143240200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:143236000-143240800	Weak transcription	Fetal Muscle Leg	muscle
33	chr4:143236000-143241600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr4:143236000-143252000	Weak transcription	HSMM	muscle
35	chr4:143236200-143237400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:143236200-143237600	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr4:143236200-143238200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:143236200-143240600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr4:143236200-143241800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr4:143236200-143243400	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr4:143236200-143245600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:143236200-143257000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr4:143236200-143257200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr4:143236200-143257600	Weak transcription	HMEC	breast
45	chr4:143236400-143239800	Weak transcription	Primary T cells from cord blood	blood
46	chr4:143236400-143244000	Weak transcription	Dnd41	blood
47	chr4:143236400-143247400	Weak transcription	Fetal Intestine Small	intestine
48	chr4:143237000-143237600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr4:143237000-143237600	Enhancers	Fetal Lung	lung
50	chr4:143237000-143237600	Enhancers	Skeletal Muscle Female	skeletal muscle

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