Variant report

Variant	rs549493329
Chromosome Location	chr1:179560937-179560938
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	MAX	chr1:179560449-179561784	MCF-7	breast:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179561299-179561309 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
2	MAX	chr1:179560515-179561699	H1-hESC	embryonic stem cell:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179561299-179561309 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
3	EP300	chr1:179560599-179561400	MCF-7	breast:	n/a	chr1:179560975-179560984 chr1:179561035-179561051 chr1:179561091-179561107 chr1:179560814-179560830 chr1:179560818-179560834 chr1:179560965-179560981
4	ESR1	chr1:179560706-179560992	T-47D	breast:	n/a	n/a
5	TEAD4	chr1:179560689-179561190	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr1:179560875-179561475	MCF-7	breast:	n/a	chr1:179561092-179561105
7	CTCF	chr1:179560615-179561099	T-47D	breast:	n/a	n/a
8	USF2	chr1:179560727-179561217	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr1:179560468-179561767	H1-hESC	embryonic stem cell:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179561299-179561309 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
10	E2F6	chr1:179560348-179561861	H1-hESC	embryonic stem cell:	n/a	chr1:179560963-179560972 chr1:179561264-179561273 chr1:179561352-179561359
11	MYC	chr1:179560835-179560952	MCF-7	breast:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
12	NR2F2	chr1:179560573-179561479	MCF-7	breast:	n/a	n/a
13	MAX	chr1:179560583-179561357	A549	lung:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179561299-179561309 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
14	MAX	chr1:179560550-179561080	H1-hESC	embryonic stem cell:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
15	E2F6	chr1:179560670-179561151	A549	lung:	n/a	chr1:179560963-179560972
16	MAX	chr1:179560418-179561505	A549	lung:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179561299-179561309 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
17	CTCF	chr1:179560889-179561231	H1-hESC	embryonic stem cell:	n/a	chr1:179561092-179561105
18	EP300	chr1:179560654-179561197	T-47D	breast:	n/a	chr1:179560975-179560984 chr1:179561035-179561051 chr1:179561091-179561107 chr1:179560814-179560830 chr1:179560818-179560834 chr1:179560965-179560981
19	GABPA	chr1:179560614-179561403	MCF-7	breast:	n/a	chr1:179560962-179560976 chr1:179560962-179560973 chr1:179560959-179560973 chr1:179560969-179560978 chr1:179560962-179560971
20	FOXA1	chr1:179560594-179561143	T-47D	breast:	n/a	n/a
21	RAD21	chr1:179560597-179561539	H1-hESC	embryonic stem cell:	n/a	n/a
22	USF1	chr1:179560634-179561150	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAX	chr1:179560364-179561745	MCF-7	breast:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179561299-179561309 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
24	CTCF	chr1:179560820-179560970	HUVEC	blood vessel:	n/a	n/a
25	MAX	chr1:179560716-179561089	ECC-1	luminal epithelium:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
26	CREB1	chr1:179560520-179561044	A549	lung:	n/a	n/a
27	TCF12	chr1:179560751-179560990	H1-hESC	embryonic stem cell:	n/a	n/a
28	ZNF143	chr1:179560708-179561535	H1-hESC	embryonic stem cell:	n/a	chr1:179560951-179560961
29	MAX	chr1:179560761-179560937	K562	blood:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
30	USF1	chr1:179560731-179561002	SK-N-SH_RA	brain:	n/a	n/a
31	CREB1	chr1:179560584-179561320	H1-hESC	embryonic stem cell:	n/a	n/a
32	E2F6	chr1:179560548-179561684	H1-hESC	embryonic stem cell:	n/a	chr1:179560963-179560972 chr1:179561264-179561273 chr1:179561352-179561359
33	TEAD4	chr1:179560686-179561130	H1-hESC	embryonic stem cell:	n/a	n/a
34	MYC	chr1:179560506-179561069	MCF10A-Er-Src	breast:	n/a	chr1:179560899-179560906 chr1:179560897-179560908 chr1:179560898-179560908 chr1:179560898-179560907 chr1:179560897-179560908 chr1:179560898-179560907
35	GATA3	chr1:179560467-179561629	MCF-7	breast:	n/a	n/a
36	CTCF	chr1:179560860-179561010	NHEK	skin:	n/a	n/a
37	CTCF	chr1:179560840-179560990	HCM	heart:	n/a	n/a
38	POLR2A	chr1:179560694-179561295	MCF-7	breast:	n/a	n/a
39	POLR2A	chr1:179560492-179561164	MCF10A-Er-Src	breast:	n/a	n/a
40	E2F6	chr1:179560476-179561313	A549	lung:	n/a	chr1:179560963-179560972 chr1:179561264-179561273
41	CTCF	chr1:179560900-179561050	SK-N-SH_RA	brain:	n/a	n/a
42	POLR2A	chr1:179560693-179561313	MCF-7	breast:	n/a	n/a
43	POLR2A	chr1:179560509-179561143	MCF10A-Er-Src	breast:	n/a	n/a
44	CTCF	chr1:179560539-179561629	MCF-7	breast:	n/a	chr1:179561092-179561105
45	TCF12	chr1:179560281-179561504	MCF-7	breast:	n/a	chr1:179561175-179561185
46	ELF1	chr1:179560552-179561672	MCF-7	breast:	n/a	chr1:179561099-179561111 chr1:179561384-179561393
47	HDAC2	chr1:179560417-179561728	MCF-7	breast:	n/a	n/a
48	POLR2A	chr1:179560738-179561012	ProgFib	skin:	n/a	n/a
49	SIN3A	chr1:179560741-179561333	H1-hESC	embryonic stem cell:	n/a	chr1:179560818-179560831 chr1:179561091-179561102
50	JUND	chr1:179560912-179561498	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179553040..179558877-chr1:179559940..179564416,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NPHS2-3	chr1:179560750-179561522	NONHSAT008198

Variant related genes	Relation type
TDRD5	TF binding region
ENSG00000227141	Chromatin interaction

Extended variants
information (count: 1 )
Associated
traits (count: 0)

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	esv3424735	chr1:179559954-179562502	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179560400-179561000	Active TSS	Duodenum Mucosa	Duodenum
2	chr1:179560400-179561000	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr1:179560400-179561400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:179560400-179561400	Bivalent Enhancer	Fetal Brain Male	brain
5	chr1:179560600-179561000	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
6	chr1:179560600-179561000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:179560600-179561000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
8	chr1:179560600-179561000	Flanking Active TSS	Right Atrium	heart
9	chr1:179560600-179561000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
10	chr1:179560600-179561200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
11	chr1:179560600-179561200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:179560600-179561200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
13	chr1:179560600-179561200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
14	chr1:179560600-179561200	Bivalent/Poised TSS	Fetal Stomach	stomach
15	chr1:179560600-179561200	Flanking Active TSS	Pancreas	Pancrea
16	chr1:179560600-179561200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
17	chr1:179560600-179561200	Bivalent/Poised TSS	NHEK	skin
18	chr1:179560600-179561400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:179560600-179561400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:179560600-179561400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:179560600-179561400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:179560600-179561400	Active TSS	Brain Anterior Caudate	brain
23	chr1:179560600-179561400	Bivalent Enhancer	Brain Cingulate Gyrus	brain
24	chr1:179560600-179561400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
25	chr1:179560600-179561400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
26	chr1:179560600-179561400	Bivalent/Poised TSS	Fetal Brain Female	brain
27	chr1:179560600-179561400	Bivalent Enhancer	Fetal Heart	heart
28	chr1:179560600-179561400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr1:179560600-179561400	Bivalent Enhancer	Spleen	Spleen
30	chr1:179560600-179561600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
31	chr1:179560600-179562000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
32	chr1:179560800-179561000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:179560800-179561000	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:179560800-179561000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:179560800-179561000	Flanking Active TSS	Esophagus	oesophagus
36	chr1:179560800-179561000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
37	chr1:179560800-179561000	Bivalent/Poised TSS	Placenta	Placenta
38	chr1:179560800-179561000	Flanking Active TSS	Gastric	stomach
39	chr1:179560800-179561000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
40	chr1:179560800-179561200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:179560800-179561200	Bivalent/Poised TSS	Primary neutrophils fromperipheralblood	blood
42	chr1:179560800-179561200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:179560800-179561200	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
44	chr1:179560800-179561200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
45	chr1:179560800-179561200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
46	chr1:179560800-179561200	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr1:179560800-179561200	Flanking Bivalent TSS/Enh	Right Ventricle	heart
48	chr1:179560800-179561400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
49	chr1:179560800-179561400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:179560800-179561400	ZNF genes & repeats	Lung	lung

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