Variant report

Variant	rs539410946
Chromosome Location	chr4:166129414-166129415
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	POLR2A	chr4:166128036-166129469	Hela-S3	cervix:	n/a	n/a
2	MAX	chr4:166128185-166129425	K562	blood:	n/a	n/a
3	MAZ	chr4:166129208-166129553	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:166128453-166129419	GM12878	blood:	n/a	n/a
5	PAX5	chr4:166128863-166129432	GM12878	blood:	n/a	chr4:166129163-166129190 chr4:166129167-166129186
6	RCOR1	chr4:166127586-166129783	IMR90	lung:	n/a	n/a
7	TBP	chr4:166128633-166129512	H1-hESC	embryonic stem cell:	n/a	n/a
8	GATA1	chr4:166128457-166129511	PBDE	blood:	n/a	n/a
9	GATA2	chr4:166128998-166129705	SH-SY5Y	brain:	n/a	chr4:166129685-166129696
10	MAZ	chr4:166127729-166129602	IMR90	lung:	n/a	n/a
11	USF1	chr4:166129395-166129706	SK-N-SH_RA	brain:	n/a	n/a
12	UBTF	chr4:166128206-166129612	K562	blood:	n/a	n/a
13	POLR2A	chr4:166128248-166129427	GM12892	blood:	n/a	n/a
14	MAZ	chr4:166128158-166129521	K562	blood:	n/a	n/a
15	ZNF143	chr4:166128549-166129454	GM12878	blood:	n/a	chr4:166129123-166129133 chr4:166129159-166129177
16	MAX	chr4:166127983-166129419	HepG2	liver:	n/a	n/a
17	RCOR1	chr4:166129196-166129511	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr4:166128145-166129531	GM19193	blood:	n/a	n/a
19	MXI1	chr4:166128108-166129488	GM12878	blood:	n/a	n/a
20	USF1	chr4:166129366-166129666	H1-hESC	embryonic stem cell:	n/a	n/a
21	RCOR1	chr4:166127429-166129772	K562	blood:	n/a	n/a
22	WRNIP1	chr4:166129253-166129629	GM12878	blood:	n/a	n/a
23	POLR2A	chr4:166128217-166129461	GM15510	blood:	n/a	n/a
24	USF1	chr4:166129414-166129694	H1-hESC	embryonic stem cell:	n/a	n/a
25	TCF7L2	chr4:166128787-166129451	Hela-S3	cervix:	n/a	n/a
26	SIN3A	chr4:166127790-166129627	H1-hESC	embryonic stem cell:	n/a	chr4:166129187-166129200 chr4:166128730-166128743 chr4:166129194-166129208 chr4:166129315-166129328
27	POLR2A	chr4:166128101-166129671	GM18505	blood:	n/a	n/a
28	POLR2A	chr4:166128077-166129835	H1-neurons	neurons:	n/a	n/a
29	POLR2A	chr4:166128343-166129454	K562	blood:	n/a	n/a
30	REST	chr4:166127627-166129571	H1-neurons	neurons:	n/a	chr4:166128899-166128912 chr4:166128722-166128729 chr4:166129315-166129328 chr4:166129128-166129148
31	MXI1	chr4:166127612-166130368	SK-N-SH	brain:	n/a	n/a
32	HA-E2F1	chr4:166128168-166129629	MCF-7	breast:	n/a	chr4:166128809-166128820
33	TBL1XR1	chr4:166128701-166129442	K562	blood:	n/a	n/a
34	POLR2A	chr4:166127726-166129782	H1-neurons	neurons:	n/a	n/a
35	ELF1	chr4:166128261-166129420	GM12878	blood:	n/a	chr4:166128745-166128758 chr4:166129121-166129133 chr4:166129190-166129202 chr4:166128748-166128757 chr4:166128747-166128758 chr4:166128747-166128758 chr4:166129147-166129159
36	GATA3	chr4:166129398-166129838	SH-SY5Y	brain:	n/a	chr4:166129685-166129696
37	EBF1	chr4:166129348-166129521	GM12878	blood:	n/a	n/a
38	TCF7L2	chr4:166128438-166129441	HCT-116	colon:	n/a	n/a
39	MAX	chr4:166127986-166129666	NB4	blood:	n/a	n/a
40	MXI1	chr4:166127890-166129958	IMR90	lung:	n/a	n/a
41	PML	chr4:166128859-166129458	GM12878	blood:	n/a	n/a
42	POLR2A	chr4:166128132-166129580	PBDE	blood:	n/a	n/a
43	POLR2A	chr4:166127962-166129444	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr4:166127788-166129477	GM12878	blood:	n/a	n/a
45	POLR2A	chr4:166127776-166129524	Raji	blood:	n/a	n/a
46	POLR2A	chr4:166128175-166129415	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:166128531..166130929-chr4:166246215..166249595,5	MCF-7	breast:
2	chr4:166126308..166130366-chr4:166247405..166251145,5	K562	blood:
3	chr4:166127800..166130090-chr4:166130347..166132969,2	MCF-7	breast:
4	chr4:166127386..166130072-chr4:166247171..166250406,6	MCF-7	breast:
5	chr4:166032812..166034984-chr4:166128697..166130341,2	K562	blood:
6	chr4:166127276..166130366-chr4:166247405..166250443,3	K562	blood:

Variant related genes	Relation type
KLHL2	TF binding region
ENSG00000052802	Chromatin interaction
ENSG00000170088	Chromatin interaction
ENSG00000109466	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv1021905	chr4:165852926-166212878	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv533191	chr4:165879671-166171638	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv881168	chr4:165975122-166196438	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	esv3357278	chr4:166127527-166130075	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
7	esv3444781	chr4:166127852-166130050	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
8	esv3341185	chr4:166127927-166130475	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:166127600-166129800	Active TSS	Colonic Mucosa	Colon
2	chr4:166127800-166129800	Active TSS	H9 Cell Line	embryonic stem cell
3	chr4:166127800-166129800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:166127800-166129800	Active TSS	Ovary	ovary
5	chr4:166127800-166130200	Active TSS	Psoas Muscle	Psoas
6	chr4:166127800-166130400	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr4:166128000-166129600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:166128000-166129600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr4:166128000-166129600	Active TSS	Gastric	stomach
10	chr4:166128000-166130000	Active TSS	Brain Hippocampus Middle	brain
11	chr4:166128000-166130000	Active TSS	A549	lung
12	chr4:166128000-166130200	Active TSS	Aorta	Aorta
13	chr4:166128000-166130200	Active TSS	Left Ventricle	heart
14	chr4:166128000-166130200	Active TSS	Right Ventricle	heart
15	chr4:166128000-166130200	Active TSS	Sigmoid Colon	Sigmoid Colon
16	chr4:166128000-166130600	Active TSS	Lung	lung
17	chr4:166128000-166131400	Active TSS	Esophagus	oesophagus
18	chr4:166128200-166129600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr4:166128200-166129600	Active TSS	Colon Smooth Muscle	Colon
20	chr4:166128200-166129600	Active TSS	Small Intestine	intestine
21	chr4:166128200-166129800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr4:166128200-166129800	Active TSS	Placenta Amnion	Placenta Amnion
23	chr4:166128200-166130000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:166128200-166130000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:166128200-166130000	Active TSS	Brain Cingulate Gyrus	brain
26	chr4:166128200-166130000	Active TSS	Rectal Smooth Muscle	rectum
27	chr4:166128200-166130200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr4:166128200-166130200	Active TSS	NHLF	lung
29	chr4:166128200-166130400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
30	chr4:166128200-166130400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
31	chr4:166128200-166130400	Active TSS	Brain Anterior Caudate	brain
32	chr4:166128200-166130400	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr4:166128200-166130600	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr4:166128200-166131000	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr4:166128400-166129600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:166128400-166129600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:166128400-166129600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:166128400-166129600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:166128400-166129600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr4:166128400-166129600	Active TSS	Primary monocytes fromperipheralblood	blood
41	chr4:166128400-166129600	Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr4:166128400-166129600	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr4:166128400-166129600	Active TSS	Duodenum Mucosa	Duodenum
44	chr4:166128400-166129600	Active TSS	Fetal Kidney	kidney
45	chr4:166128400-166129600	Active TSS	Fetal Lung	lung
46	chr4:166128400-166129600	Active TSS	Pancreas	Pancrea
47	chr4:166128400-166129600	Active TSS	Spleen	Spleen
48	chr4:166128400-166129600	Bivalent/Poised TSS	HepG2	liver
49	chr4:166128400-166129600	Active TSS	HSMMtube	muscle
50	chr4:166128400-166129800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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