Variant report

Variant	rs16843571
Chromosome Location	chr3:135684069-135684070
allele	C/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	chr3:135684044-135685250	SK-N-MC	brain:	n/a	n/a
2	SP1	chr3:135683988-135684635	A549	lung:	n/a	n/a
3	GATA3	chr3:135684057-135684460	A549	lung:	n/a	chr3:135684396-135684406
4	HA-E2F1	chr3:135683924-135685494	MCF-7	breast:	n/a	chr3:135685348-135685358 chr3:135684990-135685000 chr3:135685345-135685355 chr3:135685327-135685339 chr3:135685325-135685340 chr3:135685152-135685161 chr3:135685149-135685161
5	MXI1	chr3:135683801-135686083	SK-N-SH	brain:	n/a	n/a
6	SIN3AK20	chr3:135684024-135685525	MCF-7	breast:	n/a	n/a
7	KAP1	chr3:135683905-135684363	HEK293	kidney:	n/a	n/a
8	EGR1	chr3:135684063-135685430	HCT-116	colon:	n/a	chr3:135685153-135685166 chr3:135684987-135685000 chr3:135684987-135685000 chr3:135684990-135685000 chr3:135684983-135685005 chr3:135685270-135685280 chr3:135684987-135685000 chr3:135684988-135684999 chr3:135684990-135684999 chr3:135684987-135685000
9	SP4	chr3:135684069-135684797	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr3:135684012-135685177	ECC-1	luminal epithelium:	n/a	n/a
11	EGR1	chr3:135684028-135685374	HCT-116	colon:	n/a	chr3:135685153-135685166 chr3:135684987-135685000 chr3:135684987-135685000 chr3:135684990-135685000 chr3:135684983-135685005 chr3:135685270-135685280 chr3:135684987-135685000 chr3:135684988-135684999 chr3:135684990-135684999 chr3:135684987-135685000
12	TCF12	chr3:135684047-135685266	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr3:135684041-135685231	HCT-116	colon:	n/a	n/a
14	MXI1	chr3:135684022-135684312	H1-hESC	embryonic stem cell:	n/a	n/a
15	SIN3AK20	chr3:135684057-135684676	SK-N-SH	brain:	n/a	n/a
16	IRF1	chr3:135684029-135684229	K562	blood:	n/a	n/a
17	YY1	chr3:135684031-135684527	HCT-116	colon:	n/a	chr3:135684330-135684339 chr3:135684325-135684339
18	SIN3AK20	chr3:135683993-135684379	PANC-1	pancreas:	n/a	n/a
19	CTCF	chr3:135684020-135684170	SK-N-SH_RA	brain:	n/a	n/a
20	YY1	chr3:135684032-135684589	ECC-1	luminal epithelium:	n/a	chr3:135684330-135684339 chr3:135684325-135684339
21	STAT3	chr3:135684056-135684290	MCF10A-Er-Src	breast:	n/a	n/a
22	ZBTB7A	chr3:135684046-135684535	ECC-1	luminal epithelium:	n/a	chr3:135684304-135684315
23	YY1	chr3:135684049-135684475	SK-N-SH_RA	brain:	n/a	chr3:135684330-135684339 chr3:135684325-135684339
24	MAX	chr3:135683959-135684867	A549	lung:	n/a	n/a
25	SP1	chr3:135683998-135684627	A549	lung:	n/a	n/a
26	SMARCB1	chr3:135684056-135685396	Hela-S3	cervix:	n/a	n/a
27	MXI1	chr3:135684031-135686023	IMR90	lung:	n/a	n/a
28	ZNF143	chr3:135684048-135684678	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAZ	chr3:135683774-135685840	IMR90	lung:	n/a	n/a
30	SP1	chr3:135683876-135685271	HCT-116	colon:	n/a	chr3:135685151-135685165 chr3:135685150-135685162 chr3:135685151-135685160 chr3:135685151-135685160 chr3:135685152-135685161
31	TCF12	chr3:135683999-135684610	A549	lung:	n/a	n/a
32	SP1	chr3:135683878-135685270	HCT-116	colon:	n/a	chr3:135685151-135685165 chr3:135685150-135685162 chr3:135685151-135685160 chr3:135685151-135685160 chr3:135685152-135685161
33	E2F4	chr3:135683874-135684734	MCF10A-Er-Src	breast:	n/a	n/a
34	KAP1	chr3:135683994-135684354	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135683335..135686243-chr3:135740274..135744209,4	MCF-7	breast:
2	chr3:135678002..135681918-chr3:135682555..135686339,5	MCF-7	breast:

Variant related genes	Relation type
PPP2R3A	TF binding region
ENSG00000073711	Chromatin interaction
ENSG00000241905	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11918906	1.00[EUR][1000 genomes]
rs11925256	1.00[EUR][1000 genomes]
rs1403765	1.00[AFR][1000 genomes]
rs16843517	1.00[AFR][1000 genomes]
rs16843565	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16843592	1.00[EUR][1000 genomes]
rs16843601	1.00[AFR][1000 genomes]
rs16843602	1.00[AFR][1000 genomes]
rs16843633	1.00[EUR][1000 genomes]
rs16843656	1.00[AFR][1000 genomes]
rs16843661	1.00[EUR][1000 genomes]
rs56848754	0.91[AFR][1000 genomes]
rs57374999	1.00[EUR][1000 genomes]
rs57507646	1.00[AFR][1000 genomes]
rs57524286	1.00[AFR][1000 genomes]
rs57539640	1.00[AFR][1000 genomes]
rs57578189	1.00[AFR][1000 genomes]
rs57681844	1.00[AFR][1000 genomes]
rs58030391	1.00[EUR][1000 genomes]
rs58136416	0.83[AFR][1000 genomes]
rs58362057	1.00[AFR][1000 genomes]
rs58619345	1.00[AFR][1000 genomes]
rs59899876	1.00[AFR][1000 genomes]
rs59985031	1.00[AFR][1000 genomes]
rs60165730	1.00[EUR][1000 genomes]
rs60393211	1.00[EUR][1000 genomes]
rs61209689	1.00[EUR][1000 genomes]
rs61216931	1.00[AFR][1000 genomes]
rs72977692	0.81[AFR][1000 genomes]
rs72977699	0.81[AFR][1000 genomes]
rs72977700	0.81[AFR][1000 genomes]
rs72979626	0.91[AFR][1000 genomes]
rs72979633	0.91[AFR][1000 genomes]
rs72979636	0.91[AFR][1000 genomes]
rs72979647	1.00[AFR][1000 genomes]
rs72979686	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72979693	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72979696	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72979701	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72981430	0.83[AFR][1000 genomes]
rs72981436	1.00[AFR][1000 genomes]
rs72981447	1.00[AFR][1000 genomes]
rs72981448	1.00[AFR][1000 genomes]
rs72981456	1.00[AFR][1000 genomes]
rs72981481	1.00[EUR][1000 genomes]
rs72981494	1.00[EUR][1000 genomes]
rs72981499	1.00[AFR][1000 genomes]
rs72983403	1.00[EUR][1000 genomes]
rs72983409	1.00[EUR][1000 genomes]
rs72983435	1.00[AFR][1000 genomes]
rs72983437	1.00[EUR][1000 genomes]
rs72983449	1.00[EUR][1000 genomes]
rs72983458	1.00[AFR][1000 genomes]
rs72983460	1.00[EUR][1000 genomes]
rs72983467	0.83[AFR][1000 genomes]
rs72983501	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460860	chr3:135107678-135769006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv591829	chr3:135107678-135769006	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv829732	chr3:135561706-135756840	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	esv3374702	chr3:135649303-135686527	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3393718	chr3:135683487-135686235	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135682800-135684200	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr3:135682800-135684600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:135683000-135684200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr3:135683000-135684200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr3:135683000-135685800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr3:135683200-135684200	Enhancers	Stomach Mucosa	stomach
7	chr3:135683400-135684200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
8	chr3:135683400-135684400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:135683600-135684200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr3:135683800-135684200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr3:135683800-135684200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:135683800-135684200	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr3:135683800-135684200	Flanking Active TSS	Colon Smooth Muscle	Colon
14	chr3:135683800-135684200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr3:135683800-135685000	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
16	chr3:135683800-135685000	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
17	chr3:135683800-135685800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:135683800-135686200	Active TSS	HSMMtube	muscle
19	chr3:135683800-135687200	Active TSS	Stomach Smooth Muscle	stomach
20	chr3:135684000-135684200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
21	chr3:135684000-135684200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:135684000-135684200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:135684000-135684200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:135684000-135684200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:135684000-135684200	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr3:135684000-135684200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr3:135684000-135684200	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr3:135684000-135684200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr3:135684000-135684200	Flanking Active TSS	Liver	Liver
30	chr3:135684000-135684200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:135684000-135684200	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr3:135684000-135684200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr3:135684000-135684200	Flanking Active TSS	Fetal Heart	heart
34	chr3:135684000-135684200	Flanking Active TSS	Fetal Intestine Large	intestine
35	chr3:135684000-135684200	Flanking Active TSS	Fetal Intestine Small	intestine
36	chr3:135684000-135684200	Flanking Active TSS	Fetal Muscle Trunk	muscle
37	chr3:135684000-135684200	Flanking Active TSS	Fetal Muscle Leg	muscle
38	chr3:135684000-135684200	Enhancers	Placenta	Placenta
39	chr3:135684000-135684200	Flanking Active TSS	Rectal Smooth Muscle	rectum
40	chr3:135684000-135684200	Flanking Active TSS	NHEK	skin
41	chr3:135684000-135684400	Enhancers	Primary B cells from peripheral blood	blood
42	chr3:135684000-135684400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr3:135684000-135684400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:135684000-135684400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:135684000-135684400	Flanking Active TSS	Fetal Brain Female	brain
46	chr3:135684000-135684400	Flanking Active TSS	Pancreas	Pancrea
47	chr3:135684000-135684400	Flanking Active TSS	HUVEC	blood vessel
48	chr3:135684000-135684800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:135684000-135684800	Active TSS	Brain Germinal Matrix	brain
50	chr3:135684000-135685000	Active TSS	Primary hematopoietic stem cells	blood

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