Variant report

Variant	rs2488369
Chromosome Location	chr10:27546467-27546468
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:27546284-27546681	H1-hESC	embryonic stem cell:	n/a	n/a
2	REST	chr10:27546293-27546742	HL-60	blood:	n/a	n/a
3	POLR2A	chr10:27546260-27546778	HL-60	blood:	n/a	n/a
4	TBP	chr10:27546318-27546553	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr10:27546363-27546541	GM12878	blood:	n/a	n/a
6	SP1	chr10:27546188-27546477	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr10:27546353-27546528	GM12878	blood:	n/a	n/a
8	POLR2A	chr10:27546397-27546577	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr10:27546374-27546540	H1-hESC	embryonic stem cell:	n/a	n/a
10	NFYB	chr10:27545947-27546629	K562	blood:	n/a	n/a
11	NFYB	chr10:27546124-27546540	GM12878	blood:	n/a	n/a
12	POLR2A	chr10:27546285-27546896	HL-60	blood:	n/a	n/a
13	POLR2A	chr10:27546349-27546507	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:27546458-27546508	HNPCEpiC	eye:	n/a
2	chr10:27546458-27546508	GM12892	blood:	n/a
3	chr10:27546458-27546508	ECC-1	luminal epithelium:	n/a
4	chr10:27546458-27546508	K562	blood:	n/a
5	chr10:27546458-27546508	PrEC	prostate:	n/a
6	chr10:27546458-27546508	HMEC	breast:	n/a
7	chr10:27546458-27546508	SK-N-MC	brain:	n/a
8	chr10:27546458-27546508	MCF-7	breast:	n/a
9	chr10:27546458-27546508	AG10803	skin:	n/a
10	chr10:27546458-27546508	HCM	heart:	n/a
11	chr10:27546458-27546508	CMK	blood:	n/a
12	chr10:27546458-27546508	NHBE	bronchial:	n/a
13	chr10:27546458-27546508	PANC-1	pancreas:	n/a
14	chr10:27546458-27546508	PFSK-1	brain:	n/a
15	chr10:27546458-27546508	RPTEC	kidney:	n/a
16	chr10:27546458-27546508	MCF10A-Er-Src	breast:	n/a
17	chr10:27546458-27546508	ProgFib	skin:	n/a
18	chr10:27546458-27546508	HepG2	liver:	n/a
19	chr10:27546458-27546508	Jurkat	blood:	n/a
20	chr10:27546458-27546508	AoSMC	blood vessel:	n/a
21	chr10:27546458-27546508	HEK293	kidney:	embryo
22	chr10:27546458-27546508	LNCaP	prostate:	n/a
23	chr10:27546458-27546508	SAEC	small airway:	n/a
24	chr10:27546458-27546508	HRPEpiC	eye:	n/a
25	chr10:27546458-27546508	NB4	blood:	n/a
26	chr10:27546458-27546508	HAEpiC	amniotic membrane:	n/a
27	chr10:27546458-27546508	IMR90	lung:	fetal
28	chr10:27546458-27546508	HCPEpiC	choroid plexus:	n/a
29	chr10:27546458-27546508	BJ	skin:	n/a
30	chr10:27546458-27546508	SK-N-SH	brain:	n/a
31	chr10:27546458-27546508	HL-60	blood:	n/a
32	chr10:27546458-27546508	HUVEC	blood vessel:	n/a
33	chr10:27546458-27546508	AG09319	gingival:	n/a
34	chr10:27546458-27546508	HEEpiC	esophagus:	n/a
35	chr10:27546458-27546508	NT2-D1	testis:	n/a
36	chr10:27546458-27546508	SKMC	muscle:	n/a
37	chr10:27546458-27546508	GM12878	blood:	n/a
38	chr10:27546458-27546508	SK-N-SH_RA	brain:	n/a
39	chr10:27546458-27546508	U87	brain:	n/a
40	chr10:27546458-27546508	HCT-116	colon:	n/a
41	chr10:27546458-27546508	HRE	kidney:	n/a
42	chr10:27546458-27546508	HCF	heart:	n/a
43	chr10:27546458-27546508	HRCEpiC	kidney:	n/a
44	chr10:27546458-27546508	AG04450	lung:	fetal
45	chr10:27546458-27546508	BE2_C	brain:	n/a
46	chr10:27546458-27546508	Caco-2	colon:	n/a
47	chr10:27546458-27546508	AG09309	skin:	n/a
48	chr10:27546458-27546508	NHDF-neo	bronchial:	n/a
49	chr10:27546458-27546508	GM06990	blood:	n/a
50	chr10:27546458-27546508	Hela-S3	cervix:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:27540317..27543087-chr10:27544102..27547353,4	MCF-7	breast:

No data

Variant related genes	Relation type
ARMC4P1	TF binding region
ARMC4P1	CpG island
ENSG00000230445	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1144509	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1148169	0.95[ASN][1000 genomes]
rs1753385	0.95[ASN][1000 genomes]
rs1780090	0.83[ASN][1000 genomes]
rs1780093	0.83[ASN][1000 genomes]
rs1831186	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1831187	0.89[ASN][1000 genomes]
rs1831188	0.89[ASN][1000 genomes]
rs2104670	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2104671	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2368221	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2483499	0.91[ASN][1000 genomes]
rs2488368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2770200	0.88[ASN][1000 genomes]
rs2770201	0.83[ASN][1000 genomes]
rs2780665	0.83[ASN][1000 genomes]
rs2780669	0.83[ASN][1000 genomes]
rs2780670	0.83[ASN][1000 genomes]
rs2780671	0.83[ASN][1000 genomes]
rs2780673	0.82[ASN][1000 genomes]
rs2780677	0.82[ASN][1000 genomes]
rs2797079	0.83[ASN][1000 genomes]
rs2797080	0.95[ASN][1000 genomes]
rs2800391	0.83[ASN][1000 genomes]
rs2800393	0.83[ASN][1000 genomes]
rs2800394	0.83[ASN][1000 genomes]
rs2800395	0.83[ASN][1000 genomes]
rs2800397	0.83[ASN][1000 genomes]
rs2800398	0.82[ASN][1000 genomes]
rs2800399	0.83[ASN][1000 genomes]
rs2800402	0.82[ASN][1000 genomes]
rs2800405	0.80[ASN][1000 genomes]
rs2800407	0.95[ASN][1000 genomes]
rs35209475	0.81[ASN][1000 genomes]
rs4747595	0.80[ASN][1000 genomes]
rs480738	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs484172	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs501495	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs502416	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs527192	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs534226	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs559839	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs576161	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs590142	0.80[EUR][1000 genomes]
rs604705	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs618050	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs623380	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs624106	0.82[ASN][1000 genomes]
rs630317	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs640284	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs642428	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs642430	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs692860	0.83[EUR][1000 genomes]
rs693965	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs788212	0.81[ASN][1000 genomes]
rs788215	0.82[ASN][1000 genomes]
rs788216	0.82[ASN][1000 genomes]
rs7914155	0.83[ASN][1000 genomes]
rs7917207	0.83[ASN][1000 genomes]
rs944909	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422253	chr10:27431366-27575370	Strong transcription Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3337781	chr10:27472216-27666703	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv8614	chr10:27504487-27828406	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27538000-27547200	Weak transcription	Fetal Heart	heart
2	chr10:27541800-27546800	Weak transcription	HSMMtube	muscle
3	chr10:27542000-27547400	Weak transcription	Right Ventricle	heart
4	chr10:27542000-27547600	Weak transcription	Pancreas	Pancrea
5	chr10:27542600-27546600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr10:27545800-27547000	Enhancers	Dnd41	blood
7	chr10:27546200-27546600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
8	chr10:27546200-27546600	Active TSS	Primary T cells from cord blood	blood
9	chr10:27546200-27546600	Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr10:27546200-27546600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr10:27546400-27546600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
12	chr10:27546400-27546600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
13	chr10:27546400-27546600	Bivalent/Poised TSS	Primary T helper memory cells from peripheral blood 2	blood
14	chr10:27546400-27546600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
15	chr10:27546400-27546600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr10:27546400-27546600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
17	chr10:27546400-27546600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr10:27546400-27546600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
19	chr10:27546400-27546800	Bivalent/Poised TSS	Primary B cells from cord blood	blood
20	chr10:27546400-27547000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
21	chr10:27546400-27547200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
22	chr10:27546400-27547400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
23	chr10:27546400-27547600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
24	chr10:27546400-27547600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
25	chr10:27546400-27547600	Bivalent Enhancer	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links