Variant report

Variant	rs2298734
Chromosome Location	chr4:100816100-100816101
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:53)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:53 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:100815176-100816143	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr4:100815237-100816180	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr4:100815326-100816196	HL-60	blood:	n/a	n/a
4	POLR2A	chr4:100815015-100816148	GM12878	blood:	n/a	n/a
5	HMGN3	chr4:100815503-100816149	K562	blood:	n/a	n/a
6	POLR2A	chr4:100815167-100817274	K562	blood:	n/a	n/a
7	WRNIP1	chr4:100815009-100816163	GM12878	blood:	n/a	n/a
8	HCFC1	chr4:100815347-100816113	K562	blood:	n/a	n/a
9	MAX	chr4:100815380-100816155	NB4	blood:	n/a	n/a
10	POLR2A	chr4:100815295-100816204	PANC-1	pancreas:	n/a	n/a
11	TBP	chr4:100816065-100816144	K562	blood:	n/a	n/a
12	POLR2A	chr4:100815415-100816926	HepG2	liver:	n/a	n/a
13	POLR2A	chr4:100815190-100816203	MCF-7	breast:	n/a	n/a
14	ZMIZ1	chr4:100815420-100816159	K562	blood:	n/a	n/a
15	POLR2A	chr4:100815142-100816132	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr4:100815287-100816236	HepG2	liver:	n/a	n/a
17	POLR2A	chr4:100815286-100816288	SK-N-SH	brain:	n/a	n/a
18	ELF1	chr4:100815309-100816102	HCT-116	colon:	n/a	n/a
19	POLR2A	chr4:100815186-100816196	SK-N-MC	brain:	n/a	n/a
20	ZNF263	chr4:100814741-100816357	HEK293-T-REx	kidney:	n/a	chr4:100816100-100816109
21	RCOR1	chr4:100815383-100816181	K562	blood:	n/a	n/a
22	POLR2A	chr4:100815707-100816198	GM12878	blood:	n/a	n/a
23	CTCF	chr4:100816020-100816170	GM12864	blood:	n/a	n/a
24	POLR2A	chr4:100815099-100816174	U87	brain:	n/a	n/a
25	POLR2A	chr4:100815202-100816168	U87	brain:	n/a	n/a
26	POLR2A	chr4:100815312-100817046	GM12878	blood:	n/a	n/a
27	POLR2A	chr4:100815695-100816152	U87	brain:	n/a	n/a
28	HCFC1	chr4:100814994-100816233	Hela-S3	cervix:	n/a	n/a
29	NRF1	chr4:100815497-100816357	SK-N-SH	brain:	n/a	chr4:100815756-100815767 chr4:100815756-100815767 chr4:100815753-100815767
30	SIN3A	chr4:100814925-100816130	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr4:100815095-100816116	GM18505	blood:	n/a	n/a
32	GTF2F1	chr4:100815377-100816146	Hela-S3	cervix:	n/a	n/a
33	MAZ	chr4:100814877-100816216	IMR90	lung:	n/a	n/a
34	MTA3	chr4:100815156-100816307	GM12878	blood:	n/a	n/a
35	NFATC1	chr4:100815337-100816148	GM12878	blood:	n/a	n/a
36	REST	chr4:100814854-100816266	H1-neurons	neurons:	n/a	n/a
37	TBL1XR1	chr4:100815468-100816118	K562	blood:	n/a	n/a
38	POLR2A	chr4:100815065-100816180	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr4:100815717-100816142	SK-N-SH	brain:	n/a	n/a
40	MXI1	chr4:100814691-100816419	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr4:100815145-100816513	GM19193	blood:	n/a	n/a
42	MAZ	chr4:100815234-100816130	K562	blood:	n/a	n/a
43	POLR2A	chr4:100814765-100817025	GM12891	blood:	n/a	n/a
44	USF2	chr4:100815361-100816222	Hela-S3	cervix:	n/a	chr4:100815569-100815580
45	STAT5A	chr4:100815178-100816288	GM12878	blood:	n/a	chr4:100815358-100815370 chr4:100815784-100815791
46	POLR2A	chr4:100815724-100816163	GM12891	blood:	n/a	n/a
47	POLR2A	chr4:100815214-100816131	GM12892	blood:	n/a	n/a
48	POLR2A	chr4:100815126-100816566	GM12878	blood:	n/a	n/a
49	POLR2A	chr4:100814882-100816145	K562	blood:	n/a	n/a
50	POLR2A	chr4:100815238-100816513	Hela-S3	cervix:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:100813266..100817175-chr4:100865527..100871657,11	MCF-7	breast:
2	chr4:100814600..100817376-chr4:100869817..100872742,4	MCF-7	breast:
3	chr4:100815570..100818331-chr4:100848090..100849658,2	K562	blood:
4	chr4:100814213..100816552-chr4:100866797..100868818,3	MCF-7	breast:
5	chr4:100810623..100827791-chr4:100865444..100874425,55	K562	blood:
6	chr4:100799869..100822436-chr4:100866015..100873106,54	K562	blood:
7	chr4:100482462..100485382-chr4:100814090..100816679,3	MCF-7	breast:

No data

Variant related genes	Relation type
LAMTOR3	TF binding region
ENSG00000138823	Chromatin interaction
ENSG00000145331	Chromatin interaction
ENSG00000164031	Chromatin interaction
ENSG00000164032	Chromatin interaction
ENSG00000245322	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10001730	0.99[ASN][1000 genomes]
rs10002820	0.96[ASN][1000 genomes]
rs10014424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10016741	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10018937	0.96[ASN][1000 genomes]
rs10461176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12641552	0.85[AMR][1000 genomes]
rs1365494	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17029542	1.00[JPT][hapmap]
rs17029575	0.84[ASN][1000 genomes]
rs17029577	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17029592	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17029594	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17029606	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17029641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17029667	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17029681	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17029696	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17029698	0.89[ASN][1000 genomes]
rs17029717	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2282587	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28375729	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs28445732	0.96[ASN][1000 genomes]
rs28497573	0.96[ASN][1000 genomes]
rs28553972	0.96[ASN][1000 genomes]
rs28561548	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs28566137	0.98[ASN][1000 genomes]
rs28604943	0.98[ASN][1000 genomes]
rs28635099	0.93[ASN][1000 genomes]
rs2866175	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs28705829	0.86[ASN][1000 genomes]
rs28709045	0.89[ASN][1000 genomes]
rs28824275	0.98[ASN][1000 genomes]
rs28893880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3737485	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3775510	0.95[ASN][1000 genomes]
rs4463078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs56996205	0.82[ASN][1000 genomes]
rs57001633	0.82[ASN][1000 genomes]
rs57238114	0.95[ASN][1000 genomes]
rs57862852	0.95[ASN][1000 genomes]
rs58512740	0.84[ASN][1000 genomes]
rs58699064	0.81[ASN][1000 genomes]
rs59439986	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs59768994	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60203069	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60584294	0.84[ASN][1000 genomes]
rs60899666	0.84[ASN][1000 genomes]
rs60994806	0.95[ASN][1000 genomes]
rs61229555	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62305048	0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879661	chr4:100805207-100869635	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100813200-100816600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:100814000-100816200	Active TSS	HSMM	muscle
3	chr4:100814200-100816200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:100814200-100816200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:100814200-100816200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:100814200-100816200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:100814200-100816200	Active TSS	A549	lung
8	chr4:100814400-100816200	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr4:100814400-100816400	Active TSS	H1 Cell Line	embryonic stem cell
10	chr4:100814400-100816400	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr4:100814400-100816400	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr4:100814400-100816600	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr4:100814600-100816200	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr4:100814600-100816200	Active TSS	Muscle Satellite Cultured Cells	--
15	chr4:100814600-100816200	Active TSS	Aorta	Aorta
16	chr4:100814600-100816200	Active TSS	Fetal Muscle Trunk	muscle
17	chr4:100814600-100816200	Active TSS	Ovary	ovary
18	chr4:100814600-100816200	Active TSS	Right Atrium	heart
19	chr4:100814600-100816400	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr4:100814600-100816400	Active TSS	H9 Cell Line	embryonic stem cell
21	chr4:100814600-100816400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:100814600-100816400	Active TSS	Psoas Muscle	Psoas
23	chr4:100814800-100816200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:100814800-100816200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr4:100814800-100816200	Active TSS	Colon Smooth Muscle	Colon
26	chr4:100814800-100816200	Active TSS	Fetal Kidney	kidney
27	chr4:100814800-100816200	Active TSS	Left Ventricle	heart
28	chr4:100814800-100816200	Active TSS	Placenta Amnion	Placenta Amnion
29	chr4:100814800-100816200	Active TSS	Right Ventricle	heart
30	chr4:100814800-100816200	Active TSS	Stomach Mucosa	stomach
31	chr4:100814800-100816200	Active TSS	GM12878-XiMat	blood
32	chr4:100814800-100816400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:100814800-100816400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:100814800-100816400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:100814800-100816600	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr4:100815000-100816200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:100815000-100816200	Active TSS	Brain Hippocampus Middle	brain
38	chr4:100815000-100816200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr4:100815000-100816200	Active TSS	Colonic Mucosa	Colon
40	chr4:100815000-100816200	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr4:100815000-100816200	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr4:100815000-100816200	Active TSS	Fetal Stomach	stomach
43	chr4:100815000-100816200	Active TSS	Rectal Mucosa Donor 31	rectum
44	chr4:100815000-100816200	Active TSS	Rectal Smooth Muscle	rectum
45	chr4:100815000-100816400	Active TSS	Thymus	Thymus
46	chr4:100815000-100816600	Active TSS	Fetal Brain Female	brain
47	chr4:100815000-100816800	Active TSS	Fetal Lung	lung
48	chr4:100815200-100816200	Active TSS	Brain Cingulate Gyrus	brain
49	chr4:100815200-100816200	Active TSS	Fetal Heart	heart
50	chr4:100815200-100816400	Active TSS	Stomach Smooth Muscle	stomach

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