Variant report

Variant	rs73875504
Chromosome Location	chr4:166128087-166128088
allele	G/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	chr4:166128036-166129469	Hela-S3	cervix:	n/a	n/a
2	MAX	chr4:166128068-166129172	Hela-S3	cervix:	n/a	n/a
3	KAP1	chr4:166127562-166128357	U2OS	brain:	n/a	n/a
4	RCOR1	chr4:166127586-166129783	IMR90	lung:	n/a	n/a
5	REST	chr4:166128008-166128287	Hela-S3	cervix:	n/a	n/a
6	MAZ	chr4:166127729-166129602	IMR90	lung:	n/a	n/a
7	REST	chr4:166127992-166128323	HepG2	liver:	n/a	n/a
8	MAFF	chr4:166128069-166128361	HepG2	liver:	n/a	chr4:166128159-166128177
9	POLR2A	chr4:166128075-166128229	GM12878	blood:	n/a	n/a
10	USF2	chr4:166128046-166128199	GM12878	blood:	n/a	n/a
11	POLR2A	chr4:166128013-166129400	GM19099	blood:	n/a	n/a
12	MAX	chr4:166127983-166129419	HepG2	liver:	n/a	n/a
13	REST	chr4:166128046-166128252	PANC-1	pancreas:	n/a	n/a
14	REST	chr4:166127966-166128290	H1-hESC	embryonic stem cell:	n/a	n/a
15	CREB1	chr4:166128056-166129241	HepG2	liver:	n/a	n/a
16	MAX	chr4:166128006-166129341	H1-hESC	embryonic stem cell:	n/a	n/a
17	ZNF143	chr4:166127963-166128302	GM12878	blood:	n/a	n/a
18	ZNF263	chr4:166127798-166129262	HEK293-T-REx	kidney:	n/a	n/a
19	RCOR1	chr4:166127429-166129772	K562	blood:	n/a	n/a
20	KAP1	chr4:166127640-166128925	HEK293	kidney:	n/a	n/a
21	RCOR1	chr4:166127915-166128285	HepG2	liver:	n/a	n/a
22	MAX	chr4:166128074-166129367	GM12878	blood:	n/a	n/a
23	REST	chr4:166127891-166128230	A549	lung:	n/a	n/a
24	ELF1	chr4:166127968-166129098	HCT-116	colon:	n/a	chr4:166128745-166128758 chr4:166128748-166128757 chr4:166128747-166128758 chr4:166128747-166128758
25	TAF1	chr4:166127825-166129313	H1-neurons	neurons:	n/a	n/a
26	TEAD4	chr4:166127789-166128144	H1-hESC	embryonic stem cell:	n/a	n/a
27	SIN3A	chr4:166127790-166129627	H1-hESC	embryonic stem cell:	n/a	chr4:166129187-166129200 chr4:166128730-166128743 chr4:166129194-166129208 chr4:166129315-166129328
28	MYC	chr4:166128010-166129223	K562	blood:	n/a	n/a
29	REST	chr4:166127873-166128751	HL-60	blood:	n/a	chr4:166128722-166128729
30	POLR2A	chr4:166128077-166129835	H1-neurons	neurons:	n/a	n/a
31	STAT5A	chr4:166127973-166128534	GM12878	blood:	n/a	chr4:166128259-166128267
32	MAX	chr4:166127823-166128394	H1-hESC	embryonic stem cell:	n/a	n/a
33	MTA3	chr4:166127826-166128434	GM12878	blood:	n/a	n/a
34	REST	chr4:166127627-166129571	H1-neurons	neurons:	n/a	chr4:166128899-166128912 chr4:166128722-166128729 chr4:166129315-166129328 chr4:166129128-166129148
35	REST	chr4:166127844-166128832	ECC-1	luminal epithelium:	n/a	chr4:166128722-166128729
36	REST	chr4:166127978-166128233	PFSK-1	brain:	n/a	n/a
37	MXI1	chr4:166127612-166130368	SK-N-SH	brain:	n/a	n/a
38	WRNIP1	chr4:166127764-166128387	GM12878	blood:	n/a	n/a
39	REST	chr4:166128053-166128192	GM12878	blood:	n/a	n/a
40	POLR2A	chr4:166127758-166129366	GM18951	blood:	n/a	n/a
41	MTA3	chr4:166127764-166128523	GM12878	blood:	n/a	n/a
42	POLR2A	chr4:166127726-166129782	H1-neurons	neurons:	n/a	n/a
43	REST	chr4:166128068-166128183	K562	blood:	n/a	n/a
44	REST	chr4:166127912-166128355	GM12878	blood:	n/a	n/a
45	MAX	chr4:166127986-166129666	NB4	blood:	n/a	n/a
46	REST	chr4:166127996-166128216	HepG2	liver:	n/a	n/a
47	MXI1	chr4:166127890-166129958	IMR90	lung:	n/a	n/a
48	REST	chr4:166128035-166128231	K562	blood:	n/a	n/a
49	REST	chr4:166128070-166128233	GM12878	blood:	n/a	n/a
50	REST	chr4:166127944-166128316	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:166126308..166130366-chr4:166247405..166251145,5	K562	blood:
2	chr4:166114045..166117632-chr4:166124756..166128607,4	K562	blood:
3	chr4:166126423..166128941-chr4:166299614..166301287,2	MCF-7	breast:
4	chr4:166127800..166130090-chr4:166130347..166132969,2	MCF-7	breast:
5	chr4:166127386..166130072-chr4:166247171..166250406,6	MCF-7	breast:
6	chr4:166127276..166130366-chr4:166247405..166250443,3	K562	blood:

Variant related genes	Relation type
KLHL2	TF binding region
ENSG00000109472	Chromatin interaction
ENSG00000052802	Chromatin interaction
ENSG00000109466	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs57827554	1.00[AMR][1000 genomes]
rs59317209	1.00[AMR][1000 genomes]
rs73003881	1.00[AMR][1000 genomes]
rs73871587	1.00[AMR][1000 genomes]
rs73871590	1.00[AMR][1000 genomes]
rs73871595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73875263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv596048	chr4:166127619-166129032	Weak transcription Active TSS Flanking Active TSS Enhancers 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	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
9	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	chr4:166127200-166128400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr4:166127400-166128400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
3	chr4:166127400-166128400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr4:166127600-166128200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:166127600-166128200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:166127600-166128200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:166127600-166128200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr4:166127600-166128200	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr4:166127600-166128200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:166127600-166128200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:166127600-166128200	Flanking Active TSS	Brain Anterior Caudate	brain
12	chr4:166127600-166128200	Flanking Active TSS	Brain Cingulate Gyrus	brain
13	chr4:166127600-166128200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:166127600-166128200	Flanking Active TSS	Colon Smooth Muscle	Colon
15	chr4:166127600-166128200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr4:166127600-166128200	Flanking Active TSS	Fetal Heart	heart
17	chr4:166127600-166128200	Flanking Active TSS	Fetal Intestine Large	intestine
18	chr4:166127600-166128200	Enhancers	Small Intestine	intestine
19	chr4:166127600-166128200	Flanking Active TSS	Thymus	Thymus
20	chr4:166127600-166128200	Flanking Active TSS	NHLF	lung
21	chr4:166127600-166128400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:166127600-166128400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:166127600-166128400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
24	chr4:166127600-166128400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
25	chr4:166127600-166128400	Flanking Active TSS	Primary B cells from peripheral blood	blood
26	chr4:166127600-166128400	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr4:166127600-166128400	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr4:166127600-166128400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr4:166127600-166128400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr4:166127600-166128400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr4:166127600-166128400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr4:166127600-166128400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr4:166127600-166128400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:166127600-166128400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:166127600-166128400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:166127600-166128400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:166127600-166128400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:166127600-166128400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr4:166127600-166128400	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr4:166127600-166128400	Flanking Active TSS	Liver	Liver
41	chr4:166127600-166128400	Flanking Active TSS	Brain Angular Gyrus	brain
42	chr4:166127600-166128400	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr4:166127600-166128400	Flanking Active TSS	Fetal Brain Female	brain
44	chr4:166127600-166128400	Flanking Active TSS	Fetal Intestine Small	intestine
45	chr4:166127600-166128400	Flanking Active TSS	Fetal Muscle Leg	muscle
46	chr4:166127600-166128400	Flanking Active TSS	Fetal Stomach	stomach
47	chr4:166127600-166128400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr4:166127600-166128400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr4:166127600-166128400	Flanking Active TSS	Stomach Mucosa	stomach
50	chr4:166127600-166128400	Flanking Active TSS	Stomach Smooth Muscle	stomach

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