Variant report

Variant	rs2696345
Chromosome Location	chr2:182550149-182550150
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:56)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:56 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr2:182550084-182550279	SK-N-SH	brain:	n/a	n/a
2	RAD21	chr2:182549834-182550239	H1-hESC	embryonic stem cell:	n/a	n/a
3	REST	chr2:182549531-182550782	HL-60	blood:	n/a	chr2:182549831-182549840
4	REST	chr2:182550024-182550338	U87	brain:	n/a	n/a
5	REST	chr2:182549821-182550349	PFSK-1	brain:	n/a	chr2:182549831-182549840
6	REST	chr2:182549940-182550362	PANC-1	pancreas:	n/a	n/a
7	REST	chr2:182549656-182550598	PANC-1	pancreas:	n/a	chr2:182549831-182549840
8	REST	chr2:182549963-182550418	K562	blood:	n/a	n/a
9	POLR2A	chr2:182549480-182550456	H1-neurons	neurons:	n/a	n/a
10	REST	chr2:182549904-182550386	U87	brain:	n/a	n/a
11	REST	chr2:182549765-182550465	PANC-1	pancreas:	n/a	chr2:182549831-182549840
12	TEAD4	chr2:182549905-182550448	A549	lung:	n/a	n/a
13	REST	chr2:182550089-182550288	GM12878	blood:	n/a	n/a
14	REST	chr2:182549576-182550734	ECC-1	luminal epithelium:	n/a	chr2:182549831-182549840
15	RXRA	chr2:182549923-182550403	HepG2	liver:	n/a	n/a
16	REST	chr2:182549947-182550455	HL-60	blood:	n/a	n/a
17	GATA3	chr2:182549971-182550346	T-47D	breast:	n/a	n/a
18	REST	chr2:182549749-182550386	U87	brain:	n/a	chr2:182549831-182549840
19	POLR2A	chr2:182549441-182550206	H1-neurons	neurons:	n/a	n/a
20	REST	chr2:182549993-182550355	HepG2	liver:	n/a	n/a
21	USF2	chr2:182550068-182550268	H1-hESC	embryonic stem cell:	n/a	n/a
22	REST	chr2:182549978-182550457	HCT-116	colon:	n/a	n/a
23	REST	chr2:182550036-182550343	SK-N-SH	brain:	n/a	n/a
24	REST	chr2:182550083-182550315	Hela-S3	cervix:	n/a	n/a
25	REST	chr2:182549993-182550302	GM12878	blood:	n/a	n/a
26	REST	chr2:182549783-182550426	H1-hESC	embryonic stem cell:	n/a	chr2:182549831-182549840
27	REST	chr2:182549555-182550492	PFSK-1	brain:	n/a	chr2:182549831-182549840
28	REST	chr2:182550011-182550371	A549	lung:	n/a	n/a
29	REST	chr2:182549236-182550562	PFSK-1	brain:	n/a	chr2:182549831-182549840
30	NR2F2	chr2:182550036-182550412	MCF-7	breast:	n/a	n/a
31	REST	chr2:182549989-182550483	HCT-116	colon:	n/a	n/a
32	MXI1	chr2:182550141-182550353	H1-hESC	embryonic stem cell:	n/a	n/a
33	REST	chr2:182550055-182550330	HepG2	liver:	n/a	n/a
34	REST	chr2:182549651-182550601	ECC-1	luminal epithelium:	n/a	chr2:182549831-182549840
35	REST	chr2:182549668-182550589	MCF-7	breast:	n/a	chr2:182549831-182549840
36	REST	chr2:182550111-182550251	GM12878	blood:	n/a	n/a
37	SIN3A	chr2:182549930-182550401	H1-hESC	embryonic stem cell:	n/a	n/a
38	REST	chr2:182549914-182550414	A549	lung:	n/a	n/a
39	REST	chr2:182549929-182550399	SK-N-SH	brain:	n/a	n/a
40	RXRA	chr2:182550053-182550341	HepG2	liver:	n/a	n/a
41	SUZ12	chr2:182546965-182550375	H1-hESC	embryonic stem cell:	n/a	n/a
42	FOXA1	chr2:182550054-182550331	T-47D	breast:	n/a	n/a
43	SUZ12	chr2:182543491-182550280	NT2-D1	testis:	n/a	n/a
44	REST	chr2:182549845-182550430	MCF-7	breast:	n/a	n/a
45	ZNF143	chr2:182549943-182550356	H1-hESC	embryonic stem cell:	n/a	n/a
46	REST	chr2:182549940-182550404	GM12878	blood:	n/a	n/a
47	REST	chr2:182550062-182550352	K562	blood:	n/a	n/a
48	REST	chr2:182549837-182550401	HepG2	liver:	n/a	n/a
49	BACH1	chr2:182549836-182550406	H1-hESC	embryonic stem cell:	n/a	n/a
50	REST	chr2:182549823-182550542	PANC-1	pancreas:	n/a	chr2:182549831-182549840

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:182550098..182552555-chr2:182552964..182555197,2	K562	blood:
2	chr2:182544304..182548457-chr2:182549208..182552987,3	MCF-7	breast:
3	chr2:182546719..182548427-chr2:182548447..182551068,2	K562	blood:
4	chr2:182543026..182545649-chr2:182549552..182552304,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ITGA4-1	chr2:182549983-182550434	XLOC_001777
2	lnc-ITGA4-1	chr2:182546597-182554169	NONHSAT075881

No data

Variant related genes	Relation type
NEUROD1	TF binding region
CERKL	TF binding region
ENSG00000234595	Chromatin interaction
ENSG00000188452	Chromatin interaction
ENSG00000162992	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1000764	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10207791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10208667	0.86[EUR][1000 genomes]
rs10930976	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13398869	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13416231	0.97[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1528030	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2119517	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2583015	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2583017	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2696347	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2696351	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2950648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3856407	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3856408	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4017312	0.84[AMR][1000 genomes]
rs4666794	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4666795	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs59476732	0.92[ASN][1000 genomes]
rs60472345	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6718072	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6733263	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs732483	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7420169	0.85[YRI][hapmap]

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	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv834477	chr2:182438121-182593527	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182543600-182550200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr2:182545200-182550200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:182545200-182550400	Bivalent Enhancer	Fetal Brain Male	brain
4	chr2:182546000-182550200	Weak transcription	Gastric	stomach
5	chr2:182547000-182550200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr2:182547400-182550200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
7	chr2:182547400-182550400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
8	chr2:182547400-182550400	Bivalent Enhancer	Placenta	Placenta
9	chr2:182547600-182550200	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:182548000-182550200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
11	chr2:182548600-182550200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:182548800-182550200	Enhancers	Pancreas	Pancrea
13	chr2:182549000-182550400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
14	chr2:182549200-182550200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:182549200-182550200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr2:182549200-182550200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:182549200-182550200	Bivalent Enhancer	Brain Germinal Matrix	brain
18	chr2:182549200-182550400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:182549200-182550600	Bivalent Enhancer	Fetal Brain Female	brain
20	chr2:182549400-182550200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
21	chr2:182549400-182550200	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:182549400-182550600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
23	chr2:182549600-182550200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
24	chr2:182549600-182550200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
25	chr2:182549600-182550200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
26	chr2:182549600-182550200	Bivalent Enhancer	Spleen	Spleen
27	chr2:182549600-182550400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
28	chr2:182549800-182550200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:182549800-182550200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
30	chr2:182549800-182550200	Bivalent Enhancer	Fetal Intestine Large	intestine
31	chr2:182549800-182550200	Bivalent/Poised TSS	Right Ventricle	heart
32	chr2:182549800-182550400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:182549800-182550400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
34	chr2:182549800-182550400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
35	chr2:182550000-182550200	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:182550000-182550200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
37	chr2:182550000-182550200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
38	chr2:182550000-182550200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:182550000-182550200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
40	chr2:182550000-182550200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
41	chr2:182550000-182550200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:182550000-182550200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
43	chr2:182550000-182550200	Bivalent Enhancer	Fetal Intestine Small	intestine
44	chr2:182550000-182550200	Bivalent Enhancer	Fetal Muscle Leg	muscle
45	chr2:182550000-182550200	Bivalent Enhancer	NH-A	brain
46	chr2:182550000-182550200	Bivalent Enhancer	NHLF	lung
47	chr2:182550000-182550400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr2:182550000-182550600	Bivalent Enhancer	Brain Hippocampus Middle	brain

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