Variant report

Variant	rs28575117
Chromosome Location	chr2:99553862-99553863
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr2:99553064-99553943	H1-hESC	embryonic stem cell:	n/a	n/a
2	BACH1	chr2:99553086-99554164	H1-hESC	embryonic stem cell:	n/a	chr2:99554105-99554119
3	POLR2A	chr2:99553499-99553883	H1-neurons	neurons:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:99553830-99553880	GM12878	blood:	n/a
2	chr2:99553830-99553880	NHBE	bronchial:	n/a
3	chr2:99553830-99553880	Hepatocyte	liver:	n/a
4	chr2:99553830-99553880	A549	lung:	n/a
5	chr2:99553830-99553880	HPAEpiC	pulmonary alveolar:	n/a
6	chr2:99553830-99553880	HUVEC	blood vessel:	n/a
7	chr2:99553830-99553880	NHDF-neo	bronchial:	n/a
8	chr2:99553830-99553880	RPTEC	kidney:	n/a
9	chr2:99553830-99553880	NB4	blood:	n/a
10	chr2:99553830-99553880	HEK293	kidney:	embryo
11	chr2:99553830-99553880	GM19239	blood:	n/a
12	chr2:99553830-99553880	GM12891	blood:	n/a
13	chr2:99553830-99553880	Hela-S3	cervix:	n/a
14	chr2:99553830-99553880	HCPEpiC	choroid plexus:	n/a
15	chr2:99553830-99553880	BE2_C	brain:	n/a
16	chr2:99553830-99553880	HMEC	breast:	n/a
17	chr2:99553830-99553880	SK-N-SH	brain:	n/a
18	chr2:99553830-99553880	MCF10A-Er-Src	breast:	n/a
19	chr2:99553830-99553880	HRCEpiC	kidney:	n/a
20	chr2:99553830-99553880	AG09319	gingival:	n/a
21	chr2:99553830-99553880	CMK	blood:	n/a
22	chr2:99553830-99553880	ECC-1	luminal epithelium:	n/a
23	chr2:99553830-99553880	AG09309	skin:	n/a
24	chr2:99553830-99553880	SK-N-MC	brain:	n/a
25	chr2:99553830-99553880	SKMC	muscle:	n/a
26	chr2:99553830-99553880	SAEC	small airway:	n/a
27	chr2:99553830-99553880	Caco-2	colon:	n/a
28	chr2:99553830-99553880	PANC-1	pancreas:	n/a
29	chr2:99553830-99553880	GM06990	blood:	n/a
30	chr2:99553830-99553880	H1-hESC	embryonic stem cell:	embryo
31	chr2:99553830-99553880	SK-N-SH_RA	brain:	n/a
32	chr2:99553830-99553880	HCM	heart:	n/a
33	chr2:99553830-99553880	MCF-7	breast:	n/a
34	chr2:99553830-99553880	HCF	heart:	n/a
35	chr2:99553830-99553880	HNPCEpiC	eye:	n/a
36	chr2:99553830-99553880	HCT-116	colon:	n/a
37	chr2:99553830-99553880	U87	brain:	n/a
38	chr2:99553830-99553880	AG04450	lung:	fetal
39	chr2:99553830-99553880	IMR90	lung:	fetal
40	chr2:99553830-99553880	HepG2	liver:	n/a
41	chr2:99553830-99553880	T-47D	breast:	n/a
42	chr2:99553830-99553880	AG04449	skin:	fetal
43	chr2:99553830-99553880	HRPEpiC	eye:	n/a
44	chr2:99553830-99553880	Jurkat	blood:	n/a
45	chr2:99553830-99553880	HEEpiC	esophagus:	n/a
46	chr2:99553830-99553880	PFSK-1	brain:	n/a
47	chr2:99553830-99553880	LNCaP	prostate:	n/a
48	chr2:99553830-99553880	K562	blood:	n/a
49	chr2:99553830-99553880	HRE	kidney:	n/a
50	chr2:99553830-99553880	BJ	skin:	n/a

No data

Variant related genes	Relation type
KIAA1211L	TF binding region
KIAA1211L	CpG island

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10170063	0.83[AMR][1000 genomes]
rs10181422	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10202452	0.81[AMR][1000 genomes]
rs1115756	0.83[AMR][1000 genomes]
rs1115757	0.83[AMR][1000 genomes]
rs12470471	0.82[AMR][1000 genomes]
rs13407840	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1453564	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1530996	0.84[AMR][1000 genomes]
rs2084988	0.84[AMR][1000 genomes]
rs4585080	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4851179	0.86[AMR][1000 genomes]
rs4851183	0.88[AMR][1000 genomes]
rs62154638	0.82[AMR][1000 genomes]
rs62156558	0.83[AMR][1000 genomes]
rs6542846	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6722164	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6724476	0.88[AMR][1000 genomes]
rs6732579	0.81[AMR][1000 genomes]
rs6735801	0.84[AMR][1000 genomes]
rs6737257	0.84[AMR][1000 genomes]
rs6740054	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6740267	0.81[AMR][1000 genomes]
rs6754843	0.84[AMR][1000 genomes]
rs7570657	0.84[AMR][1000 genomes]
rs7571390	0.90[AMR][1000 genomes]
rs7586608	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7591794	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7599427	0.81[AMR][1000 genomes]
rs7605734	0.83[AMR][1000 genomes]
rs7606635	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv874697	chr2:99520608-99558970	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv834310	chr2:99533832-99709999	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv1007718	chr2:99542281-99729107	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv3339215	chr2:99550420-99554818	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3412425	chr2:99551545-99553993	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28575117	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs28575117	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs28575117	TSGA10	cis	multi-tissue	Pritchard

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99551200-99554000	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr2:99551800-99554000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:99551800-99554000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr2:99552200-99554000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr2:99552200-99554000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr2:99552200-99554000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr2:99552800-99554000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:99553000-99554000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
9	chr2:99553000-99554000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:99553200-99554000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
11	chr2:99553200-99554000	Bivalent Enhancer	Placenta	Placenta
12	chr2:99553400-99554000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr2:99553600-99554000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:99553600-99554000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
15	chr2:99553600-99554000	Enhancers	HMEC	breast
16	chr2:99553800-99554000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
17	chr2:99553800-99554000	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:99553800-99554000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
19	chr2:99553800-99554000	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
20	chr2:99553800-99554000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
21	chr2:99553800-99554000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
22	chr2:99553800-99554000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
23	chr2:99553800-99554000	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:99553800-99554000	Bivalent Enhancer	Brain Germinal Matrix	brain
25	chr2:99553800-99554000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
26	chr2:99553800-99554400	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr2:99553800-99556000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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