Variant report

Variant	rs550427717
Chromosome Location	chr5:179719621-179719622
allele	C/G
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	RFX5	chr5:179719386-179719855	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:179718769-179719935	K562	blood:	n/a	n/a
3	TCF12	chr5:179719132-179719922	A549	lung:	n/a	n/a
4	E2F6	chr5:179719163-179719825	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr5:179718819-179719692	HepG2	liver:	n/a	n/a
6	ZBTB7A	chr5:179718075-179719777	ECC-1	luminal epithelium:	n/a	chr5:179718679-179718688
7	POLR2A	chr5:179718752-179719968	H1-neurons	neurons:	n/a	n/a
8	MAZ	chr5:179717708-179721036	IMR90	lung:	n/a	chr5:179719295-179719302 chr5:179718302-179718312
9	ZBTB7A	chr5:179718292-179719881	ECC-1	luminal epithelium:	n/a	chr5:179718679-179718688
10	MAX	chr5:179719158-179719898	MCF-7	breast:	n/a	chr5:179719295-179719302
11	ZEB1	chr5:179719152-179719953	GM12878	blood:	n/a	n/a
12	ELF1	chr5:179718226-179719886	GM12878	blood:	n/a	chr5:179718858-179718867
13	NFYB	chr5:179718890-179719794	K562	blood:	n/a	chr5:179719097-179719111 chr5:179719097-179719110 chr5:179719097-179719112 chr5:179719097-179719112 chr5:179719094-179719109
14	POLR2A	chr5:179719411-179719644	A549	lung:	n/a	n/a
15	YY1	chr5:179719590-179719891	A549	lung:	n/a	chr5:179719701-179719709
16	YY1	chr5:179719463-179719910	H1-hESC	embryonic stem cell:	n/a	chr5:179719701-179719709
17	MXI1	chr5:179719521-179719862	Hela-S3	cervix:	n/a	n/a
18	CHD2	chr5:179718926-179719872	Hela-S3	cervix:	n/a	chr5:179719149-179719159
19	MXI1	chr5:179718153-179719950	IMR90	lung:	n/a	n/a
20	POLR2A	chr5:179718810-179719884	Raji	blood:	n/a	n/a
21	RCOR1	chr5:179719283-179719730	GM12878	blood:	n/a	n/a
22	MYC	chr5:179719053-179719783	K562	blood:	n/a	chr5:179719295-179719302
23	YY1	chr5:179718946-179719884	GM12892	blood:	n/a	chr5:179719701-179719709 chr5:179719122-179719136
24	MYC	chr5:179719249-179719644	MCF10A-Er-Src	breast:	n/a	chr5:179719295-179719302
25	MAZ	chr5:179718502-179719764	GM12878	blood:	n/a	chr5:179719295-179719302
26	MAX	chr5:179719083-179719859	SK-N-SH	brain:	n/a	chr5:179719295-179719302
27	POLR2A	chr5:179718827-179719828	Hela-S3	cervix:	n/a	n/a
28	MAX	chr5:179718322-179719987	HepG2	liver:	n/a	chr5:179719295-179719302
29	SIN3AK20	chr5:179719443-179719797	SK-N-SH	brain:	n/a	n/a
30	CTCF	chr5:179719540-179719690	BJ	skin:	n/a	n/a
31	CREB1	chr5:179718828-179719977	HepG2	liver:	n/a	n/a
32	EGR1	chr5:179719487-179719755	K562	blood:	n/a	chr5:179719684-179719697 chr5:179719649-179719662
33	POLR2A	chr5:179718916-179719841	ECC-1	luminal epithelium:	n/a	n/a
34	CHD2	chr5:179719528-179719702	HepG2	liver:	n/a	n/a
35	PAX5	chr5:179718956-179719746	GM12892	blood:	n/a	chr5:179719485-179719504
36	CEBPB	chr5:179719571-179720846	Hela-S3	cervix:	n/a	n/a
37	MAX	chr5:179719075-179719884	H1-hESC	embryonic stem cell:	n/a	chr5:179719295-179719302
38	USF1	chr5:179719592-179719755	GM12878	blood:	n/a	n/a
39	E2F4	chr5:179719599-179719858	MCF10A-Er-Src	breast:	n/a	n/a
40	RUNX3	chr5:179719511-179719874	GM12878	blood:	n/a	n/a
41	TAF1	chr5:179719133-179719758	HepG2	liver:	n/a	n/a
42	MAX	chr5:179719013-179719821	NB4	blood:	n/a	chr5:179719295-179719302
43	FOXP2	chr5:179719209-179719762	PFSK-1	brain:	n/a	n/a
44	CREB1	chr5:179719502-179719874	H1-hESC	embryonic stem cell:	n/a	n/a
45	TAF1	chr5:179718773-179719801	HepG2	liver:	n/a	n/a
46	POLR2A	chr5:179718802-179719911	Hela-S3	cervix:	n/a	n/a
47	UBTF	chr5:179719292-179719769	K562	blood:	n/a	n/a
48	POLR2A	chr5:179718907-179719975	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr5:179718726-179719740	GM15510	blood:	n/a	n/a
50	POLR2A	chr5:179718826-179719849	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:179718755..179721306-chr5:179919977..179922949,4	MCF-7	breast:
2	chr5:179717698..179720150-chr5:179758033..179760822,3	MCF-7	breast:
3	chr5:179683447..179685223-chr5:179718038..179720496,2	MCF-7	breast:
4	chr5:179718120..179720283-chr5:180227933..180230146,2	MCF-7	breast:
5	chr5:179718232..179719781-chr5:179756949..179759059,2	MCF-7	breast:
6	chr5:179633482..179636303-chr5:179718045..179719781,2	K562	blood:
7	chr5:179718262..179720717-chr5:180237170..180239607,2	MCF-7	breast:

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

Variant related genes	Relation type
ENSG00000248367	TF binding region
MAPK9	TF binding region
ENSG00000131459	Chromatin interaction
ENSG00000253908	Chromatin interaction
ENSG00000113300	Chromatin interaction
ENSG00000131446	Chromatin interaction
ENSG00000146090	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:13 , 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	esv3437532	chr5:179717871-179720719	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	esv3443745	chr5:179717971-179720219	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179717600-179720000	Active TSS	Brain Germinal Matrix	brain
2	chr5:179717600-179720200	Active TSS	NH-A	brain
3	chr5:179717600-179720200	Active TSS	NHLF	lung
4	chr5:179717600-179720600	Active TSS	Aorta	Aorta
5	chr5:179717800-179720000	Active TSS	Right Ventricle	heart
6	chr5:179717800-179720200	Active TSS	H1 Cell Line	embryonic stem cell
7	chr5:179717800-179720400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr5:179717800-179720400	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr5:179717800-179720600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:179717800-179720600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:179717800-179720600	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr5:179718000-179720000	Active TSS	Gastric	stomach
13	chr5:179718000-179720200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:179718000-179720200	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr5:179718000-179720200	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr5:179718000-179720200	Active TSS	Fetal Intestine Small	intestine
17	chr5:179718000-179720200	Active TSS	A549	lung
18	chr5:179718000-179720200	Active TSS	NHDF-Ad	bronchial
19	chr5:179718000-179720400	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr5:179718000-179720600	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr5:179718200-179719800	Active TSS	Small Intestine	intestine
22	chr5:179718200-179719800	Active TSS	K562	blood
23	chr5:179718200-179720000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr5:179718200-179720000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:179718200-179720000	Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr5:179718200-179720000	Active TSS	Placenta	Placenta
27	chr5:179718200-179720000	Active TSS	Psoas Muscle	Psoas
28	chr5:179718200-179720000	Active TSS	HSMMtube	muscle
29	chr5:179718200-179720200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:179718200-179720200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:179718200-179720200	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr5:179718200-179720200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:179718200-179720200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:179718200-179720200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:179718200-179720200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:179718200-179720200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr5:179718200-179720200	Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr5:179718200-179720200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
39	chr5:179718200-179720200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:179718200-179720200	Active TSS	Muscle Satellite Cultured Cells	--
41	chr5:179718200-179720200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr5:179718200-179720200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr5:179718200-179720200	Active TSS	Brain Angular Gyrus	brain
44	chr5:179718200-179720200	Active TSS	Brain Cingulate Gyrus	brain
45	chr5:179718200-179720200	Active TSS	Brain Hippocampus Middle	brain
46	chr5:179718200-179720200	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr5:179718200-179720200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr5:179718200-179720200	Active TSS	Brain Substantia Nigra	brain
49	chr5:179718200-179720200	Active TSS	Colon Smooth Muscle	Colon
50	chr5:179718200-179720200	Active TSS	Duodenum Mucosa	Duodenum

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