Variant report

Variant	rs2250207
Chromosome Location	chr20:1539689-1539690
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr20:1539641-1539691	NB4	blood:	n/a
2	chr20:1539641-1539691	NHBE	bronchial:	n/a
3	chr20:1539641-1539691	SKMC	muscle:	n/a
4	chr20:1539641-1539691	ProgFib	skin:	n/a
5	chr20:1539641-1539691	RPTEC	kidney:	n/a
6	chr20:1539641-1539691	AoSMC	blood vessel:	n/a
7	chr20:1539641-1539691	PANC-1	pancreas:	n/a
8	chr20:1539641-1539691	HRCEpiC	kidney:	n/a
9	chr20:1539641-1539691	AG10803	skin:	n/a
10	chr20:1539641-1539691	Jurkat	blood:	n/a
11	chr20:1539641-1539691	HCM	heart:	n/a
12	chr20:1539641-1539691	GM12878	blood:	n/a
13	chr20:1539641-1539691	HNPCEpiC	eye:	n/a
14	chr20:1539641-1539691	CMK	blood:	n/a
15	chr20:1539641-1539691	GM19239	blood:	n/a
16	chr20:1539641-1539691	HAEpiC	amniotic membrane:	n/a
17	chr20:1539641-1539691	HL-60	blood:	n/a
18	chr20:1539641-1539691	Hepatocyte	liver:	n/a
19	chr20:1539641-1539691	NT2-D1	testis:	n/a
20	chr20:1539641-1539691	AG09309	skin:	n/a
21	chr20:1539641-1539691	PFSK-1	brain:	n/a
22	chr20:1539641-1539691	GM12892	blood:	n/a
23	chr20:1539641-1539691	LNCaP	prostate:	n/a
24	chr20:1539641-1539691	U87	brain:	n/a
25	chr20:1539641-1539691	AG09319	gingival:	n/a
26	chr20:1539641-1539691	HRE	kidney:	n/a
27	chr20:1539641-1539691	IMR90	lung:	fetal
28	chr20:1539641-1539691	HUVEC	blood vessel:	n/a
29	chr20:1539641-1539691	HPAEpiC	pulmonary alveolar:	n/a
30	chr20:1539641-1539691	NH-A	brain:	n/a
31	chr20:1539641-1539691	AG04450	lung:	fetal
32	chr20:1539641-1539691	A549	lung:	n/a
33	chr20:1539641-1539691	NHDF-neo	bronchial:	n/a
34	chr20:1539641-1539691	MCF-7	breast:	n/a
35	chr20:1539641-1539691	H1-hESC	embryonic stem cell:	embryo
36	chr20:1539641-1539691	GM12891	blood:	n/a
37	chr20:1539641-1539691	K562	blood:	n/a
38	chr20:1539641-1539691	HCPEpiC	choroid plexus:	n/a
39	chr20:1539641-1539691	SK-N-SH	brain:	n/a
40	chr20:1539641-1539691	ECC-1	luminal epithelium:	n/a
41	chr20:1539641-1539691	T-47D	breast:	n/a
42	chr20:1539641-1539691	HCT-116	colon:	n/a
43	chr20:1539641-1539691	BJ	skin:	n/a
44	chr20:1539641-1539691	HRPEpiC	eye:	n/a
45	chr20:1539641-1539691	ovcar-3	ovarian:	n/a
46	chr20:1539641-1539691	SAEC	small airway:	n/a
47	chr20:1539641-1539691	Caco-2	colon:	n/a
48	chr20:1539641-1539691	BE2_C	brain:	n/a
49	chr20:1539641-1539691	HEK293	kidney:	embryo
50	chr20:1539641-1539691	AG04449	skin:	fetal

No data

Variant related genes	Relation type
ENSG00000242324	CpG island
SIRPD	CpG island

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2249673	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2250307	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2263652	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2263661	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2263662	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2422581	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs979673	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv2758509	chr20:1476781-1679256	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	esv2758777	chr20:1476781-1679256	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv428374	chr20:1476781-1679256	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv912596	chr20:1486637-1877150	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv1057036	chr20:1493425-1869281	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	nsv912597	chr20:1500506-1877150	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	nsv510779	chr20:1509330-1613962	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv833894	chr20:1519433-1753366	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv1063015	chr20:1531131-1674430	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv531473	chr20:1532476-1864506	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
13	nsv9775	chr20:1534985-1563660	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1532800-1545400	Weak transcription	Spleen	Spleen
2	chr20:1537000-1541200	Weak transcription	Primary T cells from cord blood	blood
3	chr20:1537000-1551600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr20:1537400-1542800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr20:1539200-1541200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr20:1539600-1542600	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links