Variant report

Variant	rs28393206
Chromosome Location	chr9:117798832-117798833
allele	C/G
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	STAT5A	chr9:117798173-117798837	GM12878	blood:	n/a	chr9:117798658-117798667
2	BCL11A	chr9:117798421-117798850	GM12878	blood:	n/a	chr9:117798658-117798667
3	CREB1	chr9:117798017-117798971	GM12878	blood:	n/a	n/a
4	EBF1	chr9:117798322-117798992	GM12878	blood:	n/a	n/a
5	ZEB1	chr9:117798200-117799238	GM12878	blood:	n/a	n/a
6	JUND	chr9:117797696-117798932	GM12878	blood:	n/a	chr9:117798660-117798671 chr9:117798659-117798666
7	ATF2	chr9:117797967-117798956	GM12878	blood:	n/a	n/a
8	EP300	chr9:117798120-117799277	GM12878	blood:	n/a	chr9:117798189-117798198 chr9:117799255-117799265 chr9:117798252-117798260
9	SPI1	chr9:117798083-117798915	GM12891	blood:	n/a	chr9:117798754-117798767 chr9:117798756-117798765 chr9:117798753-117798766
10	SP1	chr9:117798358-117798862	GM12878	blood:	n/a	n/a
11	NFIC	chr9:117797941-117799357	GM12878	blood:	n/a	n/a
12	POU2F2	chr9:117798130-117799141	GM12891	blood:	n/a	n/a
13	SPI1	chr9:117798099-117799021	GM12878	blood:	n/a	chr9:117798754-117798767 chr9:117798756-117798765 chr9:117798753-117798766
14	ATF2	chr9:117798018-117798987	GM12878	blood:	n/a	n/a
15	CEBPB	chr9:117798112-117798991	GM12878	blood:	n/a	n/a
16	RUNX3	chr9:117798027-117799288	GM12878	blood:	n/a	n/a
17	IRF4	chr9:117798310-117798958	GM12878	blood:	n/a	n/a
18	PML	chr9:117798179-117799242	GM12878	blood:	n/a	chr9:117798657-117798666
19	POLR2A	chr9:117797000-117799277	U87	brain:	n/a	n/a
20	EP300	chr9:117798052-117798846	GM12878	blood:	n/a	chr9:117798189-117798198 chr9:117798252-117798260
21	BATF	chr9:117798126-117798912	GM12878	blood:	n/a	chr9:117798656-117798666 chr9:117798655-117798666
22	BATF	chr9:117798141-117799100	GM12878	blood:	n/a	chr9:117798656-117798666 chr9:117798655-117798666
23	IKZF1	chr9:117798192-117799216	GM12878	blood:	n/a	n/a
24	BCL3	chr9:117798295-117798836	GM12878	blood:	n/a	chr9:117798658-117798667
25	TCF3	chr9:117798493-117798843	GM12878	blood:	n/a	n/a
26	IRF4	chr9:117798193-117799062	GM12878	blood:	n/a	n/a
27	CHD1	chr9:117798175-117799161	GM12878	blood:	n/a	n/a
28	EP300	chr9:117798351-117798869	GM12878	blood:	n/a	n/a
29	MTA3	chr9:117797972-117799105	GM12878	blood:	n/a	n/a
30	STAT5A	chr9:117798202-117798998	GM12878	blood:	n/a	chr9:117798658-117798667
31	POLR2A	chr9:117797006-117799277	U87	brain:	n/a	n/a
32	PAX5	chr9:117798050-117799277	GM12878	blood:	n/a	n/a
33	CUX1	chr9:117798380-117798930	GM12878	blood:	n/a	n/a
34	POU2F2	chr9:117798259-117798914	GM12891	blood:	n/a	n/a
35	NFATC1	chr9:117798345-117798924	GM12878	blood:	n/a	n/a
36	RCOR1	chr9:117798206-117798866	GM12878	blood:	n/a	n/a
37	MEF2A	chr9:117798385-117798851	GM12878	blood:	n/a	n/a
38	MTA3	chr9:117798043-117798896	GM12878	blood:	n/a	n/a
39	BCLAF1	chr9:117798089-117798882	GM12878	blood:	n/a	chr9:117798658-117798667
40	BCLAF1	chr9:117798160-117798885	GM12878	blood:	n/a	chr9:117798658-117798667
41	EBF1	chr9:117798106-117799218	GM12878	blood:	n/a	n/a
42	SMC3	chr9:117798227-117798911	GM12878	blood:	n/a	n/a
43	FOXM1	chr9:117798086-117799197	GM12878	blood:	n/a	n/a
44	EP300	chr9:117798242-117798891	GM12878	blood:	n/a	chr9:117798252-117798260
45	FOXM1	chr9:117798263-117798900	GM12878	blood:	n/a	n/a
46	RUNX3	chr9:117798034-117799241	GM12878	blood:	n/a	n/a
47	NFIC	chr9:117798014-117798944	GM12878	blood:	n/a	n/a
48	MXI1	chr9:117798189-117798971	GM12878	blood:	n/a	n/a
49	NFATC1	chr9:117798335-117798949	GM12878	blood:	n/a	n/a
50	PAX5	chr9:117798387-117798878	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
TNC	TF binding region

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

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10117421	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12336431	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12342978	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1330361	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1537011	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17241078	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17241442	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17819299	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17819466	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001357	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150101	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4549855	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56961588	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57398199	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62578423	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62578424	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62578425	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831696	chr9:117701582-117874150	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv1840787	chr9:117787173-117803882	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	esv1826575	chr9:117787173-117805719	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
6	nsv519131	chr9:117796986-117804667	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117773400-117803200	Weak transcription	Esophagus	oesophagus
2	chr9:117781800-117808600	Weak transcription	Fetal Intestine Small	intestine
3	chr9:117782400-117848200	Weak transcription	Brain Substantia Nigra	brain
4	chr9:117789000-117808600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:117791600-117833200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:117792000-117800400	Weak transcription	Fetal Lung	lung
7	chr9:117792000-117802600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:117792800-117815000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:117793200-117800600	Weak transcription	Lung	lung
10	chr9:117793600-117802600	Weak transcription	Fetal Kidney	kidney
11	chr9:117794400-117800400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr9:117794600-117799200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:117794800-117799400	Genic enhancers	Osteobl	bone
14	chr9:117795200-117803400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:117796200-117801000	Enhancers	HMEC	breast
16	chr9:117796600-117799200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:117796600-117800600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr9:117796600-117801000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr9:117797200-117799000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr9:117797200-117799000	Genic enhancers	Fetal Stomach	stomach
21	chr9:117797200-117799200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr9:117797200-117799800	Genic enhancers	NHEK	skin
23	chr9:117797200-117800800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr9:117797400-117799000	Genic enhancers	NHLF	lung
25	chr9:117797400-117799200	Enhancers	Aorta	Aorta
26	chr9:117797400-117799200	Enhancers	HSMMtube	muscle
27	chr9:117797400-117799400	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr9:117797400-117799400	Enhancers	Placenta Amnion	Placenta Amnion
29	chr9:117797400-117799400	Genic enhancers	Stomach Smooth Muscle	stomach
30	chr9:117797400-117799400	Genic enhancers	NHDF-Ad	bronchial
31	chr9:117797400-117807400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
32	chr9:117797600-117799000	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr9:117797600-117799200	Enhancers	Adipose Nuclei	Adipose
34	chr9:117797600-117799200	Enhancers	Right Ventricle	heart
35	chr9:117797600-117799200	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr9:117797800-117803400	Enhancers	Rectal Smooth Muscle	rectum
37	chr9:117798000-117799000	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr9:117798000-117799200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr9:117798000-117799600	Enhancers	Fetal Muscle Leg	muscle
40	chr9:117798200-117799000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr9:117798200-117799200	Flanking Active TSS	GM12878-XiMat	blood
42	chr9:117798200-117799600	Enhancers	NH-A	brain
43	chr9:117798200-117800400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr9:117798200-117805000	Weak transcription	HSMM	muscle
45	chr9:117798400-117799000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr9:117798400-117799200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr9:117798400-117799200	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr9:117798400-117799200	Enhancers	Brain Hippocampus Middle	brain
49	chr9:117798400-117799400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr9:117798400-117800400	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links