Variant report

Variant	rs3749796
Chromosome Location	chr5:179721376-179721377
allele	A/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	chr5:179721268-179721434	HepG2	liver:	n/a	n/a
2	CTCF	chr5:179720039-179721448	A549	lung:	n/a	chr5:179720684-179720693 chr5:179720681-179720699 chr5:179720683-179720704 chr5:179720682-179720698
3	POLR2A	chr5:179721307-179723019	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:179720972..179723069-chr5:179918796..179921248,2	MCF-7	breast:
2	chr5:179720624..179723530-chr5:179725711..179728473,2	K562	blood:
3	chr2:178298391..178298891-chr5:179720979..179721480,2	Hela-S3	cervix:
4	chr5:179720249..179721437-chr5:179755481..179756336,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNOT6-4	chr5:179719184-179722539	NONHSAT105673

Variant related genes	Relation type
MAPK9	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12654592	0.88[JPT][hapmap]
rs12655822	0.81[AMR][1000 genomes]
rs12657188	1.00[EUR][1000 genomes]
rs1363513	0.80[ASN][1000 genomes]
rs17080141	1.00[EUR][1000 genomes]
rs2042224	1.00[EUR][1000 genomes]
rs34735703	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3749795	0.83[ASN][1000 genomes]
rs4323198	1.00[GIH][hapmap];0.88[JPT][hapmap]
rs57618666	1.00[EUR][1000 genomes]
rs7447624	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	esv2758032	chr5:179534477-179729944	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv2759398	chr5:179534477-179729944	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
8	nsv883290	chr5:179712060-179818868	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	esv3398259	chr5:179717146-179721444	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv830563	chr5:179717693-179898609	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	nsv10787	chr5:179717724-179732388	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
12	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179720000-179721800	Enhancers	Gastric	stomach
2	chr5:179720000-179722800	Weak transcription	HSMMtube	muscle
3	chr5:179720000-179727400	Weak transcription	Ovary	ovary
4	chr5:179720400-179721800	Enhancers	Placenta	Placenta
5	chr5:179720400-179722200	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr5:179720400-179722200	Enhancers	Primary B cells from peripheral blood	blood
7	chr5:179720600-179721400	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr5:179720600-179721400	Weak transcription	Fetal Stomach	stomach
9	chr5:179720600-179721600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr5:179720600-179721600	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr5:179720600-179721800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr5:179720600-179722000	Enhancers	Primary B cells from cord blood	blood
13	chr5:179720600-179722200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:179720600-179722200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr5:179720600-179722200	Enhancers	Primary T cells fromperipheralblood	blood
16	chr5:179720600-179722200	Enhancers	K562	blood
17	chr5:179720600-179722400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr5:179720600-179722400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr5:179720600-179722400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr5:179720600-179722600	Enhancers	Primary hematopoietic stem cells	blood
21	chr5:179720600-179722600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:179720600-179722600	Weak transcription	Brain Germinal Matrix	brain
23	chr5:179720600-179722800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr5:179720600-179722800	Weak transcription	Colonic Mucosa	Colon
25	chr5:179720600-179723000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:179720600-179723200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr5:179720600-179723200	Weak transcription	Fetal Intestine Large	intestine
28	chr5:179720600-179724800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:179720600-179725200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:179720600-179726800	Weak transcription	Osteobl	bone
31	chr5:179720600-179727200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:179720600-179727200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr5:179720600-179727200	Weak transcription	HSMM	muscle
34	chr5:179720600-179727400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr5:179720600-179727400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr5:179720600-179727400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr5:179720600-179727600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr5:179720600-179727600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:179720600-179727600	Weak transcription	NH-A	brain
40	chr5:179720600-179727800	Weak transcription	Aorta	Aorta
41	chr5:179720600-179727800	Weak transcription	Lung	lung
42	chr5:179720600-179728200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr5:179720600-179729600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr5:179720600-179730400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr5:179720600-179731400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr5:179720600-179739200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr5:179720600-179742800	Weak transcription	Right Ventricle	heart
48	chr5:179720600-179743200	Weak transcription	Fetal Lung	lung
49	chr5:179720600-179756800	Weak transcription	NHDF-Ad	bronchial
50	chr5:179720600-179758400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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