Variant report

Variant	rs2811903
Chromosome Location	chr9:86238086-86238087
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:86237425-86238660	HEK293	kidney:	n/a	n/a
2	REST	chr9:86237616-86238804	HL-60	blood:	n/a	n/a
3	YY1	chr9:86237895-86238403	GM12891	blood:	n/a	n/a
4	CREB1	chr9:86237874-86238256	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr9:86237678-86238825	K562	blood:	n/a	n/a
6	TCF3	chr9:86237859-86238555	GM12878	blood:	n/a	n/a
7	RUNX3	chr9:86237771-86239020	GM12878	blood:	n/a	n/a
8	SIN3A	chr9:86237663-86238542	GM12878	blood:	n/a	chr9:86238495-86238506
9	POLR2A	chr9:86237659-86238855	GM12878	blood:	n/a	n/a
10	POLR2A	chr9:86237574-86238276	U87	brain:	n/a	n/a
11	ELF1	chr9:86237589-86238226	HepG2	liver:	n/a	chr9:86238187-86238199
12	BHLHE40	chr9:86237852-86238126	K562	blood:	n/a	chr9:86237988-86238004
13	TAF1	chr9:86237962-86238194	GM12891	blood:	n/a	n/a
14	ZBTB7A	chr9:86237646-86238504	ECC-1	luminal epithelium:	n/a	n/a
15	CHD1	chr9:86238062-86238251	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr9:86237625-86238817	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr9:86237627-86239010	HL-60	blood:	n/a	n/a
18	POLR2A	chr9:86237612-86239036	GM12878	blood:	n/a	n/a
19	REST	chr9:86237463-86238808	H1-neurons	neurons:	n/a	n/a
20	POLR2A	chr9:86237510-86238241	PFSK-1	brain:	n/a	n/a
21	POLR2A	chr9:86237594-86238715	U87	brain:	n/a	n/a
22	TAF1	chr9:86237875-86238211	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr9:86237506-86239610	K562	blood:	n/a	n/a
24	MAX	chr9:86237629-86238757	SK-N-SH	brain:	n/a	chr9:86238645-86238654 chr9:86238149-86238159
25	POLR2A	chr9:86237612-86238972	GM12891	blood:	n/a	n/a
26	POLR2A	chr9:86237575-86238928	MCF-7	breast:	n/a	n/a
27	MXI1	chr9:86237715-86238751	HepG2	liver:	n/a	n/a
28	FOXP2	chr9:86237689-86238209	PFSK-1	brain:	n/a	n/a
29	HNF4A	chr9:86237694-86238214	HepG2	liver:	n/a	n/a
30	MAX	chr9:86237659-86238182	K562	blood:	n/a	chr9:86238149-86238159
31	ELF1	chr9:86237469-86238344	MCF-7	breast:	n/a	chr9:86238187-86238199
32	HEY1	chr9:86237487-86239513	HepG2	liver:	n/a	chr9:86238182-86238197
33	REST	chr9:86237861-86238391	ECC-1	luminal epithelium:	n/a	n/a
34	MAX	chr9:86237415-86238860	GM12878	blood:	n/a	chr9:86238645-86238654 chr9:86238149-86238159
35	POLR2A	chr9:86237664-86238905	ECC-1	luminal epithelium:	n/a	n/a
36	POLR2A	chr9:86237597-86238956	PBDE	blood:	n/a	n/a
37	POLR2A	chr9:86237705-86238262	HepG2	liver:	n/a	n/a
38	POLR2A	chr9:86237572-86238910	GM19193	blood:	n/a	n/a
39	YY1	chr9:86237730-86238462	H1-hESC	embryonic stem cell:	n/a	n/a
40	MYC	chr9:86237725-86238910	K562	blood:	n/a	chr9:86238645-86238654 chr9:86238149-86238159
41	NR2F2	chr9:86237627-86238670	MCF-7	breast:	n/a	n/a
42	POLR2A	chr9:86237435-86238593	PFSK-1	brain:	n/a	n/a
43	CREB1	chr9:86237841-86238422	H1-hESC	embryonic stem cell:	n/a	n/a
44	TBL1XR1	chr9:86237787-86238348	GM12878	blood:	n/a	n/a
45	MXI1	chr9:86237210-86239680	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr9:86237332-86239656	GM12878	blood:	n/a	n/a
47	MAX	chr9:86237574-86238735	MCF-7	breast:	n/a	chr9:86238645-86238654 chr9:86238149-86238159
48	POLR2A	chr9:86237697-86238796	H1-hESC	embryonic stem cell:	n/a	n/a
49	MTA3	chr9:86237258-86239313	GM12878	blood:	n/a	n/a
50	TAF1	chr9:86237601-86238757	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:86237285..86238795-chr9:86535469..86537545,2	K562	blood:
2	chr9:86236918..86239524-chr9:86322198..86323756,2	K562	blood:
3	chr9:86237271..86239294-chr9:86534482..86537409,3	MCF-7	breast:
4	chr6:151712214..151713783-chr9:86237532..86239422,2	MCF-7	breast:
5	chr9:86237033..86239481-chr9:86571525..86573399,2	MCF-7	breast:
6	chr9:86236280..86241962-chr9:86320992..86325340,9	MCF-7	breast:
7	chr6:75994626..75995177-chr9:86238029..86238568,2	Hela-S3	cervix:
8	chr9:86236616..86242493-chr9:86533666..86537484,7	MCF-7	breast:

Variant related genes	Relation type
IDNK	TF binding region
ENSG00000112697	Chromatin interaction
ENSG00000225793	Chromatin interaction
ENSG00000254473	Chromatin interaction
ENSG00000165115	Chromatin interaction
ENSG00000165118	Chromatin interaction
ENSG00000181472	Chromatin interaction
ENSG00000135018	Chromatin interaction

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

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

rs_ID	r²[population]
rs10746718	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10868045	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1413293	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1572135	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1889260	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2780969	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2780972	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2780975	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2780977	0.82[EUR][1000 genomes]
rs2780978	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2780979	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2780981	0.82[EUR][1000 genomes]
rs2780982	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2811899	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2811900	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2811901	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2811902	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2811905	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2811906	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2811909	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811912	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811919	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7018643	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7874980	0.83[AMR][1000 genomes];0.87[EUR][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	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv516587	chr9:86226119-86255765	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	esv3410885	chr9:86236957-86239705	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86237200-86238400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr9:86237200-86238600	Active TSS	HSMM	muscle
3	chr9:86237200-86238600	Active TSS	NHDF-Ad	bronchial
4	chr9:86237200-86238600	Active TSS	Osteobl	bone
5	chr9:86237200-86238800	Active TSS	GM12878-XiMat	blood
6	chr9:86237200-86239000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr9:86237200-86239200	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr9:86237400-86238400	Active TSS	HMEC	breast
9	chr9:86237400-86238400	Active TSS	NH-A	brain
10	chr9:86237400-86238600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr9:86237400-86238600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:86237400-86238600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:86237400-86238600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:86237400-86238600	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr9:86237400-86238600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:86237400-86238600	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr9:86237400-86238600	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr9:86237400-86238600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:86237400-86238600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:86237400-86238600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr9:86237400-86238600	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr9:86237400-86238600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr9:86237400-86238600	Active TSS	Colon Smooth Muscle	Colon
24	chr9:86237400-86238600	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr9:86237400-86238600	Active TSS	Psoas Muscle	Psoas
26	chr9:86237400-86238600	Active TSS	Dnd41	blood
27	chr9:86237400-86238600	Active TSS	Hela-S3	cervix
28	chr9:86237400-86238600	Active TSS	HSMMtube	muscle
29	chr9:86237400-86238800	Active TSS	H9 Cell Line	embryonic stem cell
30	chr9:86237400-86238800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:86237400-86238800	Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr9:86237400-86238800	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr9:86237400-86238800	Active TSS	Aorta	Aorta
34	chr9:86237400-86238800	Active TSS	Brain Angular Gyrus	brain
35	chr9:86237400-86238800	Active TSS	Brain Germinal Matrix	brain
36	chr9:86237400-86238800	Active TSS	Fetal Kidney	kidney
37	chr9:86237400-86238800	Active TSS	Rectal Smooth Muscle	rectum
38	chr9:86237400-86238800	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr9:86237400-86238800	Active TSS	Small Intestine	intestine
40	chr9:86237400-86239000	Active TSS	H1 Cell Line	embryonic stem cell
41	chr9:86237400-86239000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr9:86237400-86239000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr9:86237400-86239000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr9:86237400-86239000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr9:86237400-86239000	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr9:86237400-86239000	Active TSS	Fetal Muscle Trunk	muscle
47	chr9:86237400-86239000	Active TSS	A549	lung
48	chr9:86237400-86239200	Active TSS	Stomach Smooth Muscle	stomach
49	chr9:86237400-86239400	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr9:86237600-86238200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links