Variant report

Variant	rs13411964
Chromosome Location	chr2:180726526-180726527
allele	A/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	ZBTB7A	chr2:180725768-180726552	ECC-1	luminal epithelium:	n/a	chr2:180725893-180725904
2	MAX	chr2:180726195-180726732	H1-hESC	embryonic stem cell:	n/a	chr2:180726718-180726728
3	POLR2A	chr2:180726170-180726542	H1-neurons	neurons:	n/a	n/a
4	MXI1	chr2:180726230-180726532	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr2:180725592-180726617	H1-hESC	embryonic stem cell:	n/a	chr2:180725755-180725765
6	HA-E2F1	chr2:180725293-180726689	MCF-7	breast:	n/a	chr2:180726650-180726657 chr2:180725720-180725729 chr2:180726086-180726096 chr2:180725945-180725957 chr2:180726102-180726111
7	NRF1	chr2:180725822-180726566	SK-N-SH	brain:	n/a	chr2:180726098-180726112 chr2:180726101-180726112 chr2:180726103-180726112 chr2:180726101-180726115
8	SIN3A	chr2:180724977-180726905	H1-hESC	embryonic stem cell:	n/a	chr2:180726076-180726087 chr2:180726083-180726096
9	TAF1	chr2:180725866-180726540	H1-hESC	embryonic stem cell:	n/a	n/a
10	CREB1	chr2:180725996-180726534	H1-hESC	embryonic stem cell:	n/a	n/a
11	KAP1	chr2:180726190-180726678	HEK293	kidney:	n/a	n/a
12	MAX	chr2:180725574-180726591	ECC-1	luminal epithelium:	n/a	chr2:180725755-180725765
13	CREB1	chr2:180726316-180726561	A549	lung:	n/a	n/a
14	RAD21	chr2:180726329-180726664	H1-hESC	embryonic stem cell:	n/a	n/a
15	ZNF263	chr2:180724559-180726526	HEK293-T-REx	kidney:	n/a	chr2:180725174-180725195
16	MAX	chr2:180726151-180726550	SK-N-SH	brain:	n/a	n/a
17	CTBP2	chr2:180725041-180726543	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr2:180725283-180726560	H1-hESC	embryonic stem cell:	n/a	chr2:180725755-180725765
19	E2F6	chr2:180725629-180726884	H1-hESC	embryonic stem cell:	n/a	chr2:180726650-180726657 chr2:180725720-180725729 chr2:180726086-180726096 chr2:180725945-180725957 chr2:180726102-180726111
20	MAX	chr2:180726054-180726550	A549	lung:	n/a	n/a
21	MAX	chr2:180725688-180726593	ECC-1	luminal epithelium:	n/a	chr2:180725755-180725765
22	E2F6	chr2:180726083-180726601	H1-hESC	embryonic stem cell:	n/a	chr2:180726086-180726096 chr2:180726102-180726111

Variant related genes	Relation type
MIR1258	TF binding region
ZNF385B	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10169684	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10205122	0.88[ASN][1000 genomes]
rs10211004	0.86[EUR][1000 genomes]
rs13407401	0.84[ASN][1000 genomes]
rs4894130	0.84[ASN][1000 genomes]
rs4894131	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56008592	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56291671	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002305	chr2:180568558-180812846	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428731	chr2:180629389-180805171	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv875472	chr2:180696414-181024926	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
4	nsv875473	chr2:180696414-181055597	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180723600-180726800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:180724200-180726600	Active TSS	Stomach Smooth Muscle	stomach
3	chr2:180724400-180727000	Active TSS	Right Atrium	heart
4	chr2:180724600-180726600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
5	chr2:180724600-180726600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:180724600-180726800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:180724600-180726800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr2:180724600-180726800	Bivalent/Poised TSS	NHDF-Ad	bronchial
9	chr2:180724600-180727000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
10	chr2:180724600-180727000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
11	chr2:180724600-180727200	Active TSS	Colon Smooth Muscle	Colon
12	chr2:180724600-180727400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr2:180724800-180726600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:180724800-180726600	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
15	chr2:180724800-180726600	Active TSS	Brain Angular Gyrus	brain
16	chr2:180724800-180726800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:180724800-180726800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
18	chr2:180724800-180726800	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr2:180724800-180726800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:180724800-180726800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
21	chr2:180724800-180726800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
22	chr2:180724800-180726800	Bivalent/Poised TSS	HSMM	muscle
23	chr2:180724800-180727000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
24	chr2:180725000-180726600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:180725000-180726600	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
26	chr2:180725000-180726800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr2:180725000-180726800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:180725000-180726800	Bivalent/Poised TSS	Colonic Mucosa	Colon
29	chr2:180725200-180726600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:180725200-180726600	Enhancers	Primary B cells from peripheral blood	blood
31	chr2:180725200-180726800	Active TSS	Gastric	stomach
32	chr2:180725200-180727000	Bivalent/Poised TSS	Fetal Brain Female	brain
33	chr2:180725400-180726600	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr2:180725400-180726600	Active TSS	Brain Substantia Nigra	brain
35	chr2:180725400-180726600	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr2:180725400-180726800	Active TSS	H9 Cell Line	embryonic stem cell
37	chr2:180725400-180726800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr2:180725400-180726800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
39	chr2:180725400-180726800	Flanking Bivalent TSS/Enh	HMEC	breast
40	chr2:180725400-180727000	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr2:180725400-180727000	Bivalent/Poised TSS	NHLF	lung
42	chr2:180725400-180727400	Active TSS	Psoas Muscle	Psoas
43	chr2:180725600-180726600	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:180725600-180726600	Bivalent/Poised TSS	Placenta Amnion	Placenta Amnion
45	chr2:180725600-180726600	Bivalent/Poised TSS	Small Intestine	intestine
46	chr2:180725600-180726600	Bivalent/Poised TSS	Thymus	Thymus
47	chr2:180725600-180726800	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr2:180725600-180726800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
49	chr2:180725600-180726800	Active TSS	Aorta	Aorta
50	chr2:180725600-180726800	Active TSS	Brain Inferior Temporal Lobe	brain

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