Variant report

Variant	rs2277421
Chromosome Location	chr13:96204808-96204809
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	CTCF	chr13:96204720-96204870	RPTEC	kidney:	n/a	chr13:96204860-96204870
2	MAX	chr13:96204532-96205345	H1-hESC	embryonic stem cell:	n/a	chr13:96205244-96205254
3	CTCF	chr13:96204791-96204896	HepG2	liver:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
4	E2F6	chr13:96204496-96205309	H1-hESC	embryonic stem cell:	n/a	chr13:96204763-96204772 chr13:96204865-96204875
5	CTCF	chr13:96204740-96204890	HRE	kidney:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
6	CTCF	chr13:96204740-96204890	GM12865	blood:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
7	CTCF	chr13:96204780-96204930	HCFaa	heart:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
8	CTCF	chr13:96204800-96204950	SAEC	small airway:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
9	CTCF	chr13:96204800-96204950	GM12867	blood:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
10	CTCF	chr13:96204800-96204950	GM12872	blood:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
11	E2F6	chr13:96204553-96205300	H1-hESC	embryonic stem cell:	n/a	chr13:96204763-96204772 chr13:96204865-96204875
12	TCF12	chr13:96204590-96204910	H1-hESC	embryonic stem cell:	n/a	chr13:96204771-96204781 chr13:96204773-96204780 chr13:96204647-96204657
13	CTCF	chr13:96204800-96204950	HAc	cerebellar:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
14	CTCF	chr13:96204780-96204930	HMEC	breast:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
15	CTCF	chr13:96204772-96204951	A549	lung:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
16	CTCF	chr13:96204760-96204910	GM12864	blood:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
17	CTCF	chr13:96204760-96204910	HUVEC	blood vessel:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
18	SP1	chr13:96204636-96205114	H1-hESC	embryonic stem cell:	n/a	chr13:96204911-96204922 chr13:96204892-96204903
19	CTCF	chr13:96204720-96204870	GM06990	blood:	n/a	chr13:96204860-96204870
20	ZBTB7A	chr13:96204770-96204881	K562	blood:	n/a	chr13:96204848-96204857 chr13:96204858-96204867
21	CTCF	chr13:96204800-96204909	HUVEC	blood vessel:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
22	RAD21	chr13:96204543-96205112	H1-hESC	embryonic stem cell:	n/a	chr13:96204993-96205007 chr13:96204859-96204869
23	POLR2A	chr13:96204666-96204840	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr13:96204740-96204890	GM06990	blood:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
25	CTCF	chr13:96204760-96204910	AG04449	skin:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
26	SP4	chr13:96204656-96205051	H1-hESC	embryonic stem cell:	n/a	chr13:96204911-96204922 chr13:96204892-96204903
27	MYC	chr13:96204774-96205026	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr13:96204720-96204870	SK-N-SH_RA	brain:	n/a	chr13:96204860-96204870
29	CTCF	chr13:96204740-96204890	GM12868	blood:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
30	CTCF	chr13:96204741-96204976	SK-N-SH_RA	brain:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
31	CTCF	chr13:96204740-96204890	GM12875	blood:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
32	RAD21	chr13:96204584-96205025	H1-hESC	embryonic stem cell:	n/a	chr13:96204993-96205007 chr13:96204859-96204869
33	SIN3A	chr13:96204371-96206220	H1-hESC	embryonic stem cell:	n/a	chr13:96205976-96205989 chr13:96204768-96204781 chr13:96205936-96205945
34	CTCF	chr13:96204800-96204950	HRPEpiC	eye:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
35	CTCF	chr13:96204740-96204890	HA-sp	spinal cord:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
36	CTBP2	chr13:96204636-96206098	H1-hESC	embryonic stem cell:	n/a	n/a
37	EGR1	chr13:96204642-96205047	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr13:96204780-96204930	HA-sp	spinal cord:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
39	CTCF	chr13:96204740-96204890	HUVEC	blood vessel:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
40	CTCF	chr13:96204800-96204950	GM12871	blood:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
41	YY1	chr13:96204670-96205175	H1-hESC	embryonic stem cell:	n/a	n/a
42	RAD21	chr13:96204745-96204914	SK-N-SH_RA	brain:	n/a	chr13:96204859-96204869
43	RAD21	chr13:96204621-96205047	H1-hESC	embryonic stem cell:	n/a	chr13:96204993-96205007 chr13:96204859-96204869
44	CTCF	chr13:96204720-96204870	GM12864	blood:	n/a	chr13:96204860-96204870
45	CTCF	chr13:96204670-96205055	H1-hESC	embryonic stem cell:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204993-96205006 chr13:96204859-96204872
46	CHD2	chr13:96204406-96205151	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr13:96204781-96204939	GM12891	blood:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
48	CTCF	chr13:96204740-96204890	HBMEC	blood vessel:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
49	CTCF	chr13:96204760-96204910	GM12866	blood:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872
50	CTCF	chr13:96204780-96204930	GM12873	blood:	n/a	chr13:96204858-96204874 chr13:96204860-96204870 chr13:96204859-96204872

Variant related genes	Relation type
CLDN10	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12583339	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12585702	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17235306	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35195129	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71433089	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]

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	nsv900933	chr13:96138087-96215289	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2277421	C2orf46	trans	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96204200-96205000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
2	chr13:96204200-96205000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr13:96204200-96206800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr13:96204400-96205000	Bivalent Enhancer	Esophagus	oesophagus
5	chr13:96204400-96205000	Bivalent Enhancer	Fetal Thymus	thymus
6	chr13:96204400-96205000	Enhancers	Gastric	stomach
7	chr13:96204400-96205600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr13:96204400-96206000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr13:96204400-96206200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
10	chr13:96204400-96206200	Bivalent Enhancer	Placenta	Placenta
11	chr13:96204400-96206200	Bivalent Enhancer	Spleen	Spleen
12	chr13:96204400-96206400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr13:96204400-96206400	Bivalent/Poised TSS	Brain Substantia Nigra	brain
14	chr13:96204400-96206600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
15	chr13:96204400-96206800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr13:96204400-96207000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr13:96204400-96207000	Active TSS	Pancreas	Pancrea
18	chr13:96204600-96205000	Bivalent/Poised TSS	Primary neutrophils fromperipheralblood	blood
19	chr13:96204600-96205000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr13:96204600-96205000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr13:96204600-96205000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
22	chr13:96204600-96205000	Bivalent Enhancer	Left Ventricle	heart
23	chr13:96204600-96205000	Active TSS	Right Ventricle	heart
24	chr13:96204600-96205200	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
25	chr13:96204600-96205200	Bivalent/Poised TSS	Thymus	Thymus
26	chr13:96204600-96205400	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr13:96204600-96205400	Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr13:96204600-96205600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr13:96204600-96205600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr13:96204600-96205600	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr13:96204600-96205600	Bivalent/Poised TSS	Fetal Brain Female	brain
32	chr13:96204600-96206000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr13:96204600-96206000	Active TSS	Right Atrium	heart
34	chr13:96204600-96206200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr13:96204600-96206200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr13:96204600-96206400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
37	chr13:96204600-96206400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
38	chr13:96204600-96206400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr13:96204600-96206600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
40	chr13:96204600-96206600	Bivalent Enhancer	Primary B cells from cord blood	blood
41	chr13:96204600-96206800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
42	chr13:96204600-96206800	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
43	chr13:96204600-96206800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
44	chr13:96204800-96205000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr13:96204800-96205000	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr13:96204800-96205000	Bivalent/Poised TSS	Colonic Mucosa	Colon
47	chr13:96204800-96205000	Bivalent Enhancer	Fetal Brain Male	brain
48	chr13:96204800-96205000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
49	chr13:96204800-96205200	Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr13:96204800-96205200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin

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