Variant report

Variant	rs55961233
Chromosome Location	chr1:210407775-210407776
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	POLR2A	chr1:210407752-210407782	H1-hESC	embryonic stem cell:	n/a	n/a
2	SMARCC1	chr1:210406586-210407990	Hela-S3	cervix:	n/a	n/a
3	TAF1	chr1:210407520-210407981	H1-neurons	neurons:	n/a	n/a
4	TCF7L2	chr1:210406960-210407876	Hela-S3	cervix:	n/a	chr1:210407431-210407441
5	POLR2A	chr1:210407548-210407963	H1-neurons	neurons:	n/a	n/a
6	TCF12	chr1:210406741-210407842	SK-N-SH	brain:	n/a	chr1:210407710-210407720
7	CTCF	chr1:210407760-210407910	HBMEC	blood vessel:	n/a	chr1:210407885-210407898 chr1:210407885-210407894
8	FOXA2	chr1:210407068-210407819	A549	lung:	n/a	chr1:210407454-210407466
9	FOXA1	chr1:210406958-210407810	T-47D	breast:	n/a	chr1:210407454-210407466
10	MAX	chr1:210407411-210407885	ECC-1	luminal epithelium:	n/a	n/a
11	MAZ	chr1:210405793-210408090	IMR90	lung:	n/a	chr1:210406540-210406549
12	MAX	chr1:210407423-210407863	H1-hESC	embryonic stem cell:	n/a	n/a
13	TCF12	chr1:210407629-210407956	H1-hESC	embryonic stem cell:	n/a	chr1:210407710-210407720
14	POLR2A	chr1:210405595-210408558	H1-neurons	neurons:	n/a	n/a
15	EGR1	chr1:210406525-210407936	HCT-116	colon:	n/a	chr1:210406906-210406919 chr1:210406948-210406962 chr1:210406906-210406919 chr1:210406569-210406579 chr1:210407621-210407636 chr1:210407621-210407635 chr1:210406900-210406913 chr1:210406906-210406919 chr1:210406906-210406919 chr1:210406907-210406918 chr1:210406901-210406923 chr1:210407623-210407633 chr1:210406907-210406917 chr1:210406905-210406920 chr1:210406631-210406641 chr1:210406907-210406917 chr1:210406903-210406917 chr1:210407623-210407632 chr1:210406905-210406919 chr1:210406895-210406905 chr1:210407622-210407635 chr1:210406907-210406916 chr1:210407623-210407634 chr1:210407622-210407635 chr1:210407622-210407635 chr1:210406906-210406916 chr1:210407622-210407635 chr1:210407617-210407639 chr1:210406564-210406577
16	HA-E2F1	chr1:210405555-210407854	MCF-7	breast:	n/a	chr1:210405557-210405566 chr1:210406562-210406577 chr1:210405978-210405988 chr1:210405975-210405985 chr1:210406950-210406960 chr1:210406620-210406632 chr1:210407579-210407589 chr1:210406572-210406581
17	TCF7L2	chr1:210406552-210407801	HCT-116	colon:	n/a	chr1:210407431-210407441
18	SIN3AK20	chr1:210406690-210408118	MCF-7	breast:	n/a	n/a
19	CTBP2	chr1:210405979-210407958	H1-hESC	embryonic stem cell:	n/a	n/a
20	NFIC	chr1:210406783-210407872	SK-N-SH	brain:	n/a	n/a
21	EGR1	chr1:210407394-210407827	HCT-116	colon:	n/a	chr1:210407621-210407636 chr1:210407621-210407635 chr1:210407623-210407633 chr1:210407623-210407632 chr1:210407622-210407635 chr1:210407623-210407634 chr1:210407622-210407635 chr1:210407622-210407635 chr1:210407622-210407635 chr1:210407617-210407639
22	SMARCB1	chr1:210406546-210407922	Hela-S3	cervix:	n/a	n/a
23	REST	chr1:210405235-210408055	H1-neurons	neurons:	n/a	n/a
24	BACH1	chr1:210407497-210407821	H1-hESC	embryonic stem cell:	n/a	n/a
25	SIN3A	chr1:210406525-210408381	H1-hESC	embryonic stem cell:	n/a	chr1:210407705-210407714 chr1:210407487-210407496 chr1:210407512-210407523
26	RAD21	chr1:210407454-210407932	H1-hESC	embryonic stem cell:	n/a	chr1:210407467-210407480 chr1:210407487-210407501 chr1:210407703-210407717
27	MAX	chr1:210406784-210407807	ECC-1	luminal epithelium:	n/a	n/a
28	EP300	chr1:210406419-210407787	SK-N-SH	brain:	n/a	chr1:210406943-210406959 chr1:210406861-210406870 chr1:210406946-210406955 chr1:210406944-210406960 chr1:210406951-210406960 chr1:210407457-210407467
29	ZNF263	chr1:210406554-210408050	HEK293-T-REx	kidney:	n/a	chr1:210407035-210407056 chr1:210406919-210406928
30	TCF12	chr1:210405200-210408026	SK-N-SH	brain:	n/a	chr1:210407710-210407720
31	CTCF	chr1:210407760-210407910	RPTEC	kidney:	n/a	chr1:210407885-210407898 chr1:210407885-210407894

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:210407755-210407805	NB4	blood:	n/a
2	chr1:210407755-210407805	BJ	skin:	n/a
3	chr1:210407755-210407805	NH-A	brain:	n/a
4	chr1:210407755-210407805	Hepatocyte	liver:	n/a
5	chr1:210407755-210407805	ovcar-3	ovarian:	n/a
6	chr1:210407755-210407805	HCF	heart:	n/a
7	chr1:210407755-210407805	HCT-116	colon:	n/a
8	chr1:210407755-210407805	PANC-1	pancreas:	n/a
9	chr1:210407755-210407805	U87	brain:	n/a
10	chr1:210407755-210407805	HNPCEpiC	eye:	n/a
11	chr1:210407755-210407805	PFSK-1	brain:	n/a
12	chr1:210407755-210407805	RPTEC	kidney:	n/a
13	chr1:210407755-210407805	HCM	heart:	n/a
14	chr1:210407755-210407805	BE2_C	brain:	n/a
15	chr1:210407755-210407805	CMK	blood:	n/a
16	chr1:210407755-210407805	HIPEpiC	eye:	n/a
17	chr1:210407755-210407805	Jurkat	blood:	n/a
18	chr1:210407755-210407805	GM12878	blood:	n/a
19	chr1:210407755-210407805	A549	lung:	n/a
20	chr1:210407755-210407805	SAEC	small airway:	n/a
21	chr1:210407755-210407805	ECC-1	luminal epithelium:	n/a
22	chr1:210407755-210407805	SK-N-SH_RA	brain:	n/a
23	chr1:210407755-210407805	HEEpiC	esophagus:	n/a
24	chr1:210407755-210407805	H1-hESC	embryonic stem cell:	embryo
25	chr1:210407755-210407805	Hela-S3	cervix:	n/a
26	chr1:210407755-210407805	GM12891	blood:	n/a
27	chr1:210407755-210407805	HCPEpiC	choroid plexus:	n/a
28	chr1:210407755-210407805	SK-N-MC	brain:	n/a
29	chr1:210407755-210407805	HRCEpiC	kidney:	n/a
30	chr1:210407755-210407805	AG09309	skin:	n/a
31	chr1:210407755-210407805	Caco-2	colon:	n/a
32	chr1:210407755-210407805	HPAEpiC	pulmonary alveolar:	n/a
33	chr1:210407755-210407805	K562	blood:	n/a
34	chr1:210407755-210407805	IMR90	lung:	fetal
35	chr1:210407755-210407805	GM12892	blood:	n/a
36	chr1:210407755-210407805	AoSMC	blood vessel:	n/a
37	chr1:210407755-210407805	HUVEC	blood vessel:	n/a
38	chr1:210407755-210407805	AG10803	skin:	n/a
39	chr1:210407755-210407805	ProgFib	skin:	n/a
40	chr1:210407755-210407805	NHDF-neo	bronchial:	n/a
41	chr1:210407755-210407805	HMEC	breast:	n/a
42	chr1:210407755-210407805	MCF10A-Er-Src	breast:	n/a
43	chr1:210407755-210407805	LNCaP	prostate:	n/a
44	chr1:210407755-210407805	AG04449	skin:	fetal
45	chr1:210407755-210407805	SK-N-SH	brain:	n/a
46	chr1:210407755-210407805	HL-60	blood:	n/a
47	chr1:210407755-210407805	HRE	kidney:	n/a
48	chr1:210407755-210407805	HRPEpiC	eye:	n/a
49	chr1:210407755-210407805	T-47D	breast:	n/a
50	chr1:210407755-210407805	GM06990	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:210405800..210407964-chr1:210502205..210503882,2	MCF-7	breast:
2	chr1:210404317..210408653-chr1:210545033..210548956,7	MCF-7	breast:
3	chr1:210405867..210408909-chr1:210535692..210538632,3	MCF-7	breast:
4	chr1:210406407..210409749-chr1:210545963..210547821,3	MCF-7	breast:
5	chr1:210407733..210410508-chr1:210422643..210424269,2	MCF-7	breast:

Variant related genes	Relation type
SERTAD4-AS1	TF binding region
SERTAD4	TF binding region
SERTAD4-AS1	CpG island
SERTAD4	CpG island
ENSG00000054392	Chromatin interaction
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12239511	1.00[EUR][1000 genomes]
rs56195858	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59599798	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6670548	1.00[EUR][1000 genomes]
rs73063762	1.00[EUR][1000 genomes]
rs74156118	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210405400-210407800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:210405400-210407800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr1:210405400-210407800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr1:210405400-210407800	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr1:210405400-210407800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
6	chr1:210405400-210407800	Active TSS	Colon Smooth Muscle	Colon
7	chr1:210405400-210407800	Active TSS	Rectal Smooth Muscle	rectum
8	chr1:210405400-210408000	Bivalent Enhancer	Fetal Brain Male	brain
9	chr1:210405400-210408000	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr1:210405600-210407800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:210405600-210407800	Active TSS	H9 Cell Line	embryonic stem cell
12	chr1:210405600-210407800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:210405600-210407800	Active TSS	Aorta	Aorta
14	chr1:210405600-210407800	Active TSS	Brain Anterior Caudate	brain
15	chr1:210405600-210407800	Active TSS	Brain Substantia Nigra	brain
16	chr1:210405600-210407800	Active TSS	Placenta Amnion	Placenta Amnion
17	chr1:210405600-210407800	Active TSS	NHDF-Ad	bronchial
18	chr1:210405800-210407800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr1:210405800-210407800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
20	chr1:210405800-210407800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
21	chr1:210405800-210407800	Active TSS	Brain Hippocampus Middle	brain
22	chr1:210405800-210407800	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr1:210406000-210407800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:210406000-210407800	Active TSS	Fetal Kidney	kidney
25	chr1:210406000-210407800	Active TSS	Gastric	stomach
26	chr1:210406000-210407800	Bivalent/Poised TSS	HepG2	liver
27	chr1:210406200-210408400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
28	chr1:210406400-210407800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:210406400-210407800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:210406400-210407800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:210406400-210408000	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr1:210406400-210408200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
33	chr1:210406600-210407800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:210406600-210407800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
35	chr1:210406600-210407800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
36	chr1:210406600-210407800	Flanking Bivalent TSS/Enh	Osteobl	bone
37	chr1:210406600-210408000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
38	chr1:210406600-210408000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
39	chr1:210406600-210408000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
40	chr1:210406600-210408000	Flanking Active TSS	HMEC	breast
41	chr1:210406800-210407800	Bivalent Enhancer	Spleen	Spleen
42	chr1:210406800-210408000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:210406800-210408200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:210407000-210407800	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:210407000-210407800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
46	chr1:210407000-210407800	Bivalent Enhancer	Stomach Mucosa	stomach
47	chr1:210407000-210408000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
48	chr1:210407000-210408000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr1:210407000-210408000	Bivalent Enhancer	Liver	Liver
50	chr1:210407000-210408000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain

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