Variant report

Variant	rs10858022
Chromosome Location	chr1:114446341-114446342
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr1:114446196-114446495	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:114446190-114448381	GM18505	blood:	n/a	n/a
3	MAX	chr1:114445917-114448671	MCF-7	breast:	n/a	chr1:114448611-114448620 chr1:114447122-114447131
4	MXI1	chr1:114446060-114448767	SK-N-SH	brain:	n/a	n/a
5	NR2F2	chr1:114446295-114448569	K562	blood:	n/a	n/a
6	JUND	chr1:114446322-114448706	MCF-7	breast:	n/a	chr1:114447429-114447440 chr1:114446687-114446701
7	SPI1	chr1:114446050-114446381	GM12891	blood:	n/a	n/a
8	MAZ	chr1:114446193-114448140	GM12878	blood:	n/a	chr1:114447122-114447131
9	POLR2A	chr1:114446320-114448436	GM19099	blood:	n/a	n/a
10	GABPA	chr1:114446317-114448796	MCF-7	breast:	n/a	n/a
11	MYC	chr1:114446293-114448475	K562	blood:	n/a	chr1:114447122-114447131
12	MAX	chr1:114446149-114448674	MCF-7	breast:	n/a	chr1:114448611-114448620 chr1:114447122-114447131
13	RCOR1	chr1:114446180-114448135	GM12878	blood:	n/a	n/a
14	PML	chr1:114446225-114448700	MCF-7	breast:	n/a	n/a
15	TBP	chr1:114446235-114448108	GM12878	blood:	n/a	n/a
16	EP300	chr1:114446179-114446465	GM12878	blood:	n/a	n/a
17	JUN	chr1:114445974-114448749	K562	blood:	n/a	chr1:114446687-114446701
18	STAT3	chr1:114446187-114446501	GM12878	blood:	n/a	n/a
19	SIN3AK20	chr1:114445935-114448789	MCF-7	breast:	n/a	n/a
20	POLR2A	chr1:114446267-114446346	MCF10A-Er-Src	breast:	n/a	n/a
21	SIN3AK20	chr1:114445852-114449210	MCF-7	breast:	n/a	n/a
22	WRNIP1	chr1:114446281-114448508	GM12878	blood:	n/a	n/a
23	MTA3	chr1:114446311-114448522	GM12878	blood:	n/a	n/a
24	JUND	chr1:114446326-114448505	K562	blood:	n/a	chr1:114447429-114447440 chr1:114446687-114446701
25	HDAC2	chr1:114445980-114448756	MCF-7	breast:	n/a	n/a
26	POLR2A	chr1:114446088-114448562	GM12891	blood:	n/a	n/a
27	SPI1	chr1:114445968-114446511	HL-60	blood:	n/a	n/a
28	EBF1	chr1:114446221-114446975	GM12878	blood:	n/a	chr1:114446540-114446551
29	SPI1	chr1:114446054-114446360	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:114446026-114448464	GM12878	blood:	n/a	n/a
31	CEBPB	chr1:114446129-114448738	MCF-7	breast:	n/a	n/a
32	NR2F2	chr1:114446024-114448746	MCF-7	breast:	n/a	n/a
33	PML	chr1:114446232-114448498	GM12878	blood:	n/a	n/a
34	ELF1	chr1:114446225-114448742	MCF-7	breast:	n/a	n/a
35	GABPA	chr1:114446004-114448722	MCF-7	breast:	n/a	n/a
36	TBL1XR1	chr1:114446261-114446553	GM12878	blood:	n/a	n/a
37	RELA	chr1:114446179-114448245	GM15510	blood:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114445859..114448805-chr17:42295421..42298283,3	MCF-7	breast:
2	chr1:114446008..114448199-chr1:114495493..114497584,2	MCF-7	breast:
3	chr1:114361850..114364464-chr1:114444259..114447022,2	MCF-7	breast:
4	chr1:114352137..114357235-chr1:114445065..114452395,18	MCF-7	breast:
5	chr1:114299428..114302166-chr1:114446012..114448303,2	K562	blood:
6	chr1:114444168..114452207-chr1:114466193..114476714,61	K562	blood:
7	chr1:114353683..114357770-chr1:114446246..114449576,8	K562	blood:
8	chr1:114445068..114448942-chr1:115050232..115055017,4	MCF-7	breast:
9	chr1:114446165..114448738-chr1:115053730..115055909,2	MCF-7	breast:
10	chr1:114446144..114448333-chr19:16187175..16189942,2	MCF-7	breast:
11	chr1:114300712..114302958-chr1:114446093..114449659,3	MCF-7	breast:
12	chr1:114445771..114447458-chr9:132251917..132254040,2	MCF-7	breast:
13	chr1:114352306..114358140-chr1:114445806..114450844,18	MCF-7	breast:
14	chr1:114300422..114303875-chr1:114445198..114448512,7	MCF-7	breast:
15	chr1:114353620..114357151-chr1:114445438..114449458,6	K562	blood:

No data

Variant related genes	Relation type
AP4B1	TF binding region
DCLRE1B	TF binding region
ENSG00000235527	Chromatin interaction
ENSG00000116793	Chromatin interaction
ENSG00000108312	Chromatin interaction
ENSG00000197323	Chromatin interaction
ENSG00000134242	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000081019	Chromatin interaction
ENSG00000204054	Chromatin interaction
ENSG00000231128	Chromatin interaction
ENSG00000167460	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10745340	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10776775	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10858023	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11102701	0.81[AFR][1000 genomes]
rs11582409	0.85[YRI][hapmap]
rs11584821	0.85[YRI][hapmap]
rs1217382	0.87[YRI][hapmap]
rs1217391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1217392	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17464525	1.00[YRI][hapmap]
rs17510162	0.85[YRI][hapmap]
rs3765598	0.85[YRI][hapmap]
rs3789613	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3811021	0.85[YRI][hapmap]
rs3827733	0.85[YRI][hapmap]
rs6661817	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700802	0.85[YRI][hapmap]
rs7523862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7524200	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114415000-114447000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:114420200-114446400	Weak transcription	Aorta	Aorta
3	chr1:114435600-114446400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:114436000-114446800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:114436200-114446600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:114436200-114446600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:114436800-114446400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr1:114437600-114446400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:114439200-114446400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:114440800-114446400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:114441000-114446600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:114441200-114446400	Weak transcription	Fetal Brain Male	brain
13	chr1:114441200-114446400	Weak transcription	A549	lung
14	chr1:114442200-114446400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
15	chr1:114443000-114446400	Weak transcription	HSMMtube	muscle
16	chr1:114443000-114446600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:114443000-114446600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:114443000-114446600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:114443000-114446600	Weak transcription	Lung	lung
20	chr1:114443000-114446600	Weak transcription	Pancreas	Pancrea
21	chr1:114443000-114446800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:114443000-114446800	Weak transcription	Ovary	ovary
23	chr1:114443400-114446400	Enhancers	Fetal Intestine Large	intestine
24	chr1:114443400-114446600	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr1:114443800-114446600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:114444000-114446400	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr1:114444000-114446600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr1:114444200-114446600	Genic enhancers	Primary T cells fromperipheralblood	blood
29	chr1:114444400-114446600	Weak transcription	Placenta	Placenta
30	chr1:114444600-114446400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:114444600-114446400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:114444600-114446600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:114444800-114446400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:114445000-114446400	Weak transcription	Right Atrium	heart
35	chr1:114445400-114446600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr1:114445400-114446600	Weak transcription	Esophagus	oesophagus
37	chr1:114445400-114446600	Weak transcription	Left Ventricle	heart
38	chr1:114445400-114446600	Enhancers	Stomach Mucosa	stomach
39	chr1:114445400-114446800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:114445400-114446800	Weak transcription	Spleen	Spleen
41	chr1:114445600-114446400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:114445600-114446400	Enhancers	Primary B cells from peripheral blood	blood
43	chr1:114445600-114446400	Enhancers	Primary hematopoietic stem cells	blood
44	chr1:114445600-114446400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr1:114445600-114446400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr1:114445600-114446400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:114445600-114446400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:114445600-114446400	Enhancers	Brain Anterior Caudate	brain
49	chr1:114445600-114446400	Weak transcription	Fetal Muscle Leg	muscle
50	chr1:114445600-114446400	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links