Variant report

Variant	rs35264204
Chromosome Location	chr3:142298272-142298273
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:46)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:46 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr3:142296938-142298318	MCF-7	breast:	n/a	n/a
2	MTA3	chr3:142296982-142298737	GM12878	blood:	n/a	n/a
3	MXI1	chr3:142297007-142298484	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:142297265-142298328	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:142296959-142298595	GM18505	blood:	n/a	n/a
6	POLR2A	chr3:142297125-142298432	GM18951	blood:	n/a	n/a
7	KAP1	chr3:142297289-142298344	U2OS	brain:	n/a	n/a
8	ATF2	chr3:142297242-142298410	GM12878	blood:	n/a	n/a
9	PML	chr3:142296841-142298327	GM12878	blood:	n/a	n/a
10	YY1	chr3:142297084-142298392	SK-N-SH	brain:	n/a	chr3:142297370-142297381 chr3:142297742-142297751
11	MXI1	chr3:142296408-142298719	SK-N-SH	brain:	n/a	n/a
12	RELA	chr3:142297196-142298280	GM15510	blood:	n/a	n/a
13	POLR2A	chr3:142296667-142298686	GM12891	blood:	n/a	n/a
14	POLR2A	chr3:142296817-142298665	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr3:142295895-142298691	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr3:142296847-142298351	IMR90	lung:	n/a	n/a
17	SMC3	chr3:142297819-142298384	HepG2	liver:	n/a	n/a
18	STAT5A	chr3:142296975-142298434	GM12878	blood:	n/a	chr3:142297093-142297104 chr3:142297123-142297146 chr3:142297411-142297423
19	POLR2A	chr3:142297335-142298314	GM12878	blood:	n/a	n/a
20	MXI1	chr3:142296459-142298498	IMR90	lung:	n/a	n/a
21	SIN3A	chr3:142297113-142298309	GM12878	blood:	n/a	n/a
22	CUX1	chr3:142297675-142298531	K562	blood:	n/a	n/a
23	POLR2A	chr3:142297187-142298681	GM12878	blood:	n/a	n/a
24	TCF12	chr3:142296897-142298293	A549	lung:	n/a	chr3:142297402-142297412
25	IRF1	chr3:142297403-142298492	K562	blood:	n/a	chr3:142297834-142297845 chr3:142297741-142297755
26	MAZ	chr3:142296267-142298684	IMR90	lung:	n/a	n/a
27	IRF1	chr3:142297351-142298430	K562	blood:	n/a	chr3:142297834-142297845 chr3:142297741-142297755
28	POLR2A	chr3:142297075-142298596	GM19099	blood:	n/a	n/a
29	TBL1XR1	chr3:142297464-142298488	K562	blood:	n/a	n/a
30	SIN3A	chr3:142296838-142298370	H1-hESC	embryonic stem cell:	n/a	n/a
31	FOSL2	chr3:142297206-142298283	A549	lung:	n/a	n/a
32	HCFC1	chr3:142296097-142298628	Hela-S3	cervix:	n/a	n/a
33	SMARCC1	chr3:142296913-142298571	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr3:142296866-142298572	GM12892	blood:	n/a	n/a
35	POLR2A	chr3:142298247-142298652	GM12892	blood:	n/a	n/a
36	JUN	chr3:142296436-142298710	K562	blood:	n/a	chr3:142297145-142297154 chr3:142296991-142297000 chr3:142296499-142296508
37	MAX	chr3:142296521-142298279	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr3:142296736-142298655	GM12878	blood:	n/a	n/a
39	POLR2A	chr3:142296737-142298608	Hela-S3	cervix:	n/a	n/a
40	MYC	chr3:142297134-142298470	K562	blood:	n/a	n/a
41	POLR2A	chr3:142297242-142298468	PBDE	blood:	n/a	n/a
42	GTF2F1	chr3:142296968-142298599	Hela-S3	cervix:	n/a	n/a
43	CHD1	chr3:142297252-142298392	GM12878	blood:	n/a	n/a
44	TAF1	chr3:142296930-142298318	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr3:142297163-142298399	HL-60	blood:	n/a	n/a
46	POLR2A	chr3:142297099-142298313	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:142297806..142298379-chr5:1524091..1524637,2	NB4	blood:
2	chr3:142297625..142299268-chr3:142441632..142444151,3	K562	blood:
3	chr3:142280626..142282527-chr3:142296623..142299039,2	K562	blood:
4	chr12:46753334..46754030-chr3:142297866..142298600,2	Hela-S3	cervix:
5	chr3:142297403..142299294-chr3:142720282..142722143,3	MCF-7	breast:
6	chr3:142296149..142300233-chr3:142313670..142315817,6	K562	blood:
7	chr3:142297466..142299799-chr3:142313558..142315620,3	K562	blood:
8	chr3:142295918..142298932-chr3:142719049..142722504,4	MCF-7	breast:
9	chr3:142280626..142283157-chr3:142296079..142299039,3	K562	blood:
10	chr3:142297625..142299268-chr3:142441632..142445353,4	K562	blood:
11	chr13:98628143..98628846-chr3:142297511..142298310,2	NB4	blood:
12	chr3:142217843..142219879-chr3:142296547..142298953,2	MCF-7	breast:
13	chr3:142294568..142300006-chr3:142310942..142319455,13	MCF-7	breast:
14	chr3:142296202..142300183-chr3:142719946..142722583,4	K562	blood:
15	chr3:142294183..142301262-chr3:142311308..142318922,13	MCF-7	breast:
16	chr3:142295888..142299099-chr3:142720440..142723490,3	K562	blood:
17	chr3:142297949..142299634-chr3:142710792..142712643,2	MCF-7	breast:
18	chr3:142296891..142299259-chr3:142680803..142682548,2	K562	blood:

No data

Variant related genes	Relation type
ATR	TF binding region
RPL6P9	TF binding region
ENSG00000268129	Chromatin interaction
ENSG00000175054	Chromatin interaction
ENSG00000144935	Chromatin interaction
ENSG00000188582	Chromatin interaction
ENSG00000163714	Chromatin interaction
ENSG00000065150	Chromatin interaction
ENSG00000241570	Chromatin interaction
ENSG00000120756	Chromatin interaction
ENSG00000153395	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs28897764	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28897765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28910270	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28910271	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28910272	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34104088	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs34213965	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34383865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34678750	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34686786	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35363608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35404216	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35440390	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35988759	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35993426	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36090479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv591919	chr3:142219542-142308070	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142293800-142298400	Active TSS	GM12878-XiMat	blood
2	chr3:142296000-142298400	Active TSS	K562	blood
3	chr3:142296200-142298400	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr3:142296200-142298400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:142296200-142298400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:142296200-142298400	Active TSS	Psoas Muscle	Psoas
7	chr3:142296200-142298400	Active TSS	Stomach Smooth Muscle	stomach
8	chr3:142296200-142298600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:142296400-142298400	Active TSS	H1 Cell Line	embryonic stem cell
10	chr3:142296400-142298400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:142296400-142298400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:142296400-142298400	Active TSS	Colonic Mucosa	Colon
13	chr3:142296400-142298400	Active TSS	Fetal Intestine Large	intestine
14	chr3:142296400-142298400	Active TSS	Right Ventricle	heart
15	chr3:142296400-142298400	Active TSS	HSMMtube	muscle
16	chr3:142296400-142298400	Active TSS	NHDF-Ad	bronchial
17	chr3:142296400-142298600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:142296600-142298400	Active TSS	H9 Cell Line	embryonic stem cell
19	chr3:142296600-142298400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:142296600-142298400	Active TSS	Fetal Muscle Trunk	muscle
21	chr3:142296600-142298600	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr3:142296600-142298600	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr3:142296800-142298400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr3:142296800-142298400	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr3:142296800-142298400	Active TSS	Muscle Satellite Cultured Cells	--
26	chr3:142296800-142298400	Active TSS	Fetal Stomach	stomach
27	chr3:142296800-142298400	Active TSS	HMEC	breast
28	chr3:142296800-142298400	Active TSS	HSMM	muscle
29	chr3:142296800-142298600	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr3:142296800-142298600	Active TSS	Stomach Mucosa	stomach
31	chr3:142296800-142298800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:142297000-142298400	Active TSS	Brain Hippocampus Middle	brain
33	chr3:142297000-142298400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:142297000-142298400	Active TSS	Fetal Brain Female	brain
35	chr3:142297000-142298400	Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr3:142297000-142298600	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr3:142297000-142298800	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr3:142297000-142298800	Active TSS	Rectal Smooth Muscle	rectum
39	chr3:142297200-142298400	Active TSS	Adipose Nuclei	Adipose
40	chr3:142297200-142298600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:142297200-142298800	Active TSS	Thymus	Thymus
42	chr3:142297400-142298400	Active TSS	Primary T cells fromperipheralblood	blood
43	chr3:142297600-142298400	Active TSS	Brain Germinal Matrix	brain
44	chr3:142297600-142298600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:142297800-142298600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:142298000-142298400	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr3:142298000-142298400	Flanking Active TSS	Primary B cells from peripheral blood	blood
48	chr3:142298000-142298400	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr3:142298000-142298400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr3:142298000-142298400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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