Variant report

Variant	rs4864685
Chromosome Location	chr4:53728338-53728339
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	chr4:53728077-53728771	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr4:53728112-53728741	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:53728066-53728690	GM19099	blood:	n/a	n/a
4	RCOR1	chr4:53727953-53728884	K562	blood:	n/a	n/a
5	TCF12	chr4:53728032-53728852	ECC-1	luminal epithelium:	n/a	chr4:53728218-53728228
6	CTCF	chr4:53728260-53728410	Caco-2	colon:	n/a	n/a
7	POLR2A	chr4:53728008-53728835	MCF-7	breast:	n/a	n/a
8	CTCF	chr4:53728240-53728390	HCT-116	colon:	n/a	n/a
9	ZBTB7A	chr4:53728207-53728467	K562	blood:	n/a	n/a
10	CTCF	chr4:53728220-53728370	HBMEC	blood vessel:	n/a	n/a
11	EGR1	chr4:53727993-53728525	K562	blood:	n/a	chr4:53728435-53728445 chr4:53728430-53728443 chr4:53728430-53728443 chr4:53728429-53728444
12	CTCF	chr4:53728240-53728390	SK-N-SH_RA	brain:	n/a	n/a
13	FOXP2	chr4:53727997-53728715	PFSK-1	brain:	n/a	n/a
14	CTCF	chr4:53728300-53728450	SK-N-SH_RA	brain:	n/a	n/a
15	E2F6	chr4:53728252-53728517	K562	blood:	n/a	chr4:53728435-53728444 chr4:53728439-53728449
16	POLR2A	chr4:53728162-53728543	A549	lung:	n/a	n/a
17	RAD21	chr4:53728025-53728698	ECC-1	luminal epithelium:	n/a	n/a
18	MAX	chr4:53728284-53728867	K562	blood:	n/a	chr4:53728303-53728313 chr4:53728433-53728443
19	YY1	chr4:53728142-53728868	K562	blood:	n/a	chr4:53728295-53728304 chr4:53728435-53728449 chr4:53728435-53728444 chr4:53728147-53728161 chr4:53728463-53728477 chr4:53728150-53728164 chr4:53728296-53728310 chr4:53728438-53728452 chr4:53728266-53728280
20	HEY1	chr4:53728156-53728633	K562	blood:	n/a	n/a
21	TBP	chr4:53727916-53728704	K562	blood:	n/a	n/a
22	BHLHE40	chr4:53728327-53728352	K562	blood:	n/a	n/a
23	HA-E2F1	chr4:53727679-53728844	MCF-7	breast:	n/a	chr4:53728200-53728210 chr4:53728435-53728444 chr4:53728439-53728449
24	POLR2A	chr4:53728005-53728708	GM12892	blood:	n/a	n/a
25	CTCF	chr4:53728260-53728410	AG10803	skin:	n/a	n/a
26	CTCF	chr4:53728325-53728399	GM10266	blood:	n/a	n/a
27	CTCF	chr4:53728240-53728390	HMF	breast:	n/a	n/a
28	MYC	chr4:53728224-53728837	MCF10A-Er-Src	breast:	n/a	chr4:53728303-53728313 chr4:53728433-53728443
29	CTCF	chr4:53728334-53728403	GM12892	blood:	n/a	n/a
30	CTCF	chr4:53728235-53728565	IMR90	lung:	n/a	n/a
31	POLR2A	chr4:53728137-53728695	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr4:53728015-53728704	ProgFib	skin:	n/a	n/a
33	RAD21	chr4:53727978-53728887	SK-N-SH_RA	brain:	n/a	n/a
34	ZBTB7A	chr4:53727992-53728512	ECC-1	luminal epithelium:	n/a	n/a
35	HEY1	chr4:53728161-53728613	HepG2	liver:	n/a	n/a
36	POLR2A	chr4:53728131-53728516	HepG2	liver:	n/a	n/a
37	TAF1	chr4:53728266-53728692	H1-neurons	neurons:	n/a	n/a
38	CTCF	chr4:53728200-53728350	BJ	skin:	n/a	n/a
39	RAD21	chr4:53728266-53728448	K562	blood:	n/a	n/a
40	CTCF	chr4:53728299-53728474	GM13976	blood:	n/a	n/a
41	CTCF	chr4:53728260-53728410	HRPEpiC	eye:	n/a	n/a
42	E2F6	chr4:53727459-53729023	H1-hESC	embryonic stem cell:	n/a	chr4:53728200-53728210 chr4:53728643-53728654 chr4:53728435-53728444 chr4:53728439-53728449
43	POLR2A	chr4:53728148-53729427	H1-hESC	embryonic stem cell:	n/a	n/a
44	CREB1	chr4:53728111-53728851	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr4:53728097-53728583	HUVEC	blood vessel:	n/a	n/a
46	GTF2F1	chr4:53728320-53728711	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr4:53728042-53728612	GM12878	blood:	n/a	n/a
48	CTCF	chr4:53728171-53728585	GM12878	blood:	n/a	n/a
49	HMGN3	chr4:53728013-53729012	K562	blood:	n/a	n/a
50	MAZ	chr4:53727966-53728744	K562	blood:	n/a	chr4:53728303-53728313 chr4:53728433-53728443

No.	Distal block	Cell Line	Cell type
1	chr4:53525430..53527688-chr4:53726700..53729187,4	MCF-7	breast:
2	chr4:53586938..53589965-chr4:53727574..53731676,3	MCF-7	breast:
3	chr4:53577401..53580169-chr4:53726393..53730142,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCFD2-2	chr4:53728251-53728352	NONHSAT096385

Variant related genes	Relation type
RASL11B	TF binding region
ENSG00000109189	Chromatin interaction
ENSG00000264585	Chromatin interaction
ENSG00000248866	Chromatin interaction
ENSG00000212588	Chromatin interaction
ENSG00000226950	Chromatin interaction
ENSG00000248375	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10003908	0.80[AMR][1000 genomes]
rs10016904	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10023440	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10026162	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10032190	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11940896	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11941841	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11947787	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4864678	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4864680	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62336790	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62336795	0.84[EUR][1000 genomes]
rs62338810	0.86[ASN][1000 genomes]
rs6554056	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6844680	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs730246	0.82[AMR][1000 genomes]
rs730247	0.82[AMR][1000 genomes]
rs731073	0.82[AMR][1000 genomes]
rs7663943	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7692692	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8287	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs881743	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs936690	0.83[AMR][1000 genomes]
rs962416	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9995861	0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1004086	chr4:53698581-53773183	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3360858	chr4:53727420-53729968	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53727400-53729600	Active TSS	Brain Angular Gyrus	brain
2	chr4:53727400-53729600	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr4:53727600-53728400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
4	chr4:53727600-53728600	Bivalent/Poised TSS	Colonic Mucosa	Colon
5	chr4:53727600-53728800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
6	chr4:53727600-53728800	Active TSS	Brain Substantia Nigra	brain
7	chr4:53727600-53728800	Active TSS	Psoas Muscle	Psoas
8	chr4:53727600-53729200	Active TSS	H9 Cell Line	embryonic stem cell
9	chr4:53727600-53729200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
10	chr4:53727600-53729200	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr4:53727600-53729600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr4:53727600-53729600	Active TSS	NHDF-Ad	bronchial
13	chr4:53727800-53728400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
14	chr4:53727800-53728600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:53727800-53728600	Bivalent/Poised TSS	NHLF	lung
16	chr4:53727800-53728800	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr4:53727800-53729000	Flanking Bivalent TSS/Enh	Liver	Liver
18	chr4:53727800-53729200	Flanking Active TSS	HMEC	breast
19	chr4:53727800-53729400	Flanking Active TSS	Pancreas	Pancrea
20	chr4:53727800-53730800	Active TSS	Aorta	Aorta
21	chr4:53727800-53731800	Active TSS	Fetal Kidney	kidney
22	chr4:53728000-53728400	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr4:53728000-53728600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
24	chr4:53728000-53728600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr4:53728000-53728600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
26	chr4:53728000-53728600	Active TSS	Brain Hippocampus Middle	brain
27	chr4:53728000-53728600	Active TSS	Colon Smooth Muscle	Colon
28	chr4:53728000-53728600	Active TSS	Esophagus	oesophagus
29	chr4:53728000-53728600	Active TSS	Placenta Amnion	Placenta Amnion
30	chr4:53728000-53728600	Transcr. at gene 5' and 3'	Right Atrium	heart
31	chr4:53728000-53728600	Active TSS	Sigmoid Colon	Sigmoid Colon
32	chr4:53728000-53728600	Bivalent/Poised TSS	Thymus	Thymus
33	chr4:53728000-53728800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:53728000-53728800	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr4:53728000-53728800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:53728000-53728800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:53728000-53728800	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr4:53728000-53728800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:53728000-53728800	Active TSS	Primary T cells from cord blood	blood
40	chr4:53728000-53728800	Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr4:53728000-53728800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr4:53728000-53728800	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr4:53728000-53728800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr4:53728000-53728800	Active TSS	Brain Anterior Caudate	brain
45	chr4:53728000-53728800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr4:53728000-53728800	Active TSS	Rectal Smooth Muscle	rectum
47	chr4:53728000-53728800	Active TSS	Small Intestine	intestine
48	chr4:53728000-53728800	Active TSS	Stomach Mucosa	stomach
49	chr4:53728000-53728800	Active TSS	HepG2	liver
50	chr4:53728000-53729000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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