Variant report

Variant	rs9988633
Chromosome Location	chr1:47798577-47798578
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:47797779-47800924	HepG2	liver:	n/a	n/a
2	JUND	chr1:47798548-47800744	K562	blood:	n/a	chr1:47799978-47799987
3	CBX3	chr1:47798411-47799849	K562	blood:	n/a	n/a
4	POLR2A	chr1:47798393-47801213	K562	blood:	n/a	n/a
5	TBL1XR1	chr1:47798424-47798899	K562	blood:	n/a	n/a
6	POLR2A	chr1:47798152-47800857	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:47798390-47800831	IMR90	lung:	n/a	n/a
8	POLR2A	chr1:47798571-47800813	GM12891	blood:	n/a	n/a
9	BHLHE40	chr1:47798531-47800811	K562	blood:	n/a	chr1:47799793-47799809
10	MXI1	chr1:47798380-47801138	IMR90	lung:	n/a	n/a
11	ZNF384	chr1:47798520-47798862	K562	blood:	n/a	n/a
12	POLR2A	chr1:47798487-47798735	K562	blood:	n/a	n/a
13	POLR2A	chr1:47798403-47801305	K562	blood:	n/a	n/a
14	MXI1	chr1:47798187-47800866	SK-N-SH	brain:	n/a	n/a
15	REST	chr1:47798449-47800990	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	chr1:47798576-47798626	SK-N-MC	brain:	n/a
2	chr1:47798576-47798626	K562	blood:	n/a
3	chr1:47798576-47798626	A549	lung:	n/a
4	chr1:47798576-47798626	AG09309	skin:	n/a
5	chr1:47798576-47798626	NHDF-neo	bronchial:	n/a
6	chr1:47798576-47798626	PANC-1	pancreas:	n/a
7	chr1:47798576-47798626	GM19239	blood:	n/a
8	chr1:47798576-47798626	MCF-7	breast:	n/a
9	chr1:47798576-47798626	HRE	kidney:	n/a
10	chr1:47798576-47798626	CMK	blood:	n/a
11	chr1:47798576-47798626	AG04449	skin:	fetal
12	chr1:47798576-47798626	HepG2	liver:	n/a
13	chr1:47798576-47798626	HMEC	breast:	n/a
14	chr1:47798576-47798626	AG04450	lung:	fetal
15	chr1:47798576-47798626	HIPEpiC	eye:	n/a
16	chr1:47798576-47798626	GM12891	blood:	n/a
17	chr1:47798576-47798626	GM12892	blood:	n/a
18	chr1:47798576-47798626	BE2_C	brain:	n/a
19	chr1:47798576-47798626	LNCaP	prostate:	n/a
20	chr1:47798576-47798626	HNPCEpiC	eye:	n/a
21	chr1:47798576-47798626	NB4	blood:	n/a
22	chr1:47798576-47798626	H1-hESC	embryonic stem cell:	embryo
23	chr1:47798576-47798626	GM12878	blood:	n/a
24	chr1:47798576-47798626	PrEC	prostate:	n/a
25	chr1:47798576-47798626	SAEC	small airway:	n/a
26	chr1:47798576-47798626	PFSK-1	brain:	n/a
27	chr1:47798576-47798626	ovcar-3	ovarian:	n/a
28	chr1:47798576-47798626	HUVEC	blood vessel:	n/a
29	chr1:47798576-47798626	HEEpiC	esophagus:	n/a
30	chr1:47798576-47798626	AoSMC	blood vessel:	n/a
31	chr1:47798576-47798626	HCT-116	colon:	n/a
32	chr1:47798576-47798626	SKMC	muscle:	n/a
33	chr1:47798576-47798626	AG10803	skin:	n/a
34	chr1:47798576-47798626	ECC-1	luminal epithelium:	n/a
35	chr1:47798576-47798626	AG09319	gingival:	n/a
36	chr1:47798576-47798626	Hela-S3	cervix:	n/a
37	chr1:47798576-47798626	Hepatocyte	liver:	n/a
38	chr1:47798576-47798626	HRCEpiC	kidney:	n/a
39	chr1:47798576-47798626	IMR90	lung:	fetal
40	chr1:47798576-47798626	RPTEC	kidney:	n/a
41	chr1:47798576-47798626	ProgFib	skin:	n/a
42	chr1:47798576-47798626	HCPEpiC	choroid plexus:	n/a
43	chr1:47798576-47798626	HL-60	blood:	n/a
44	chr1:47798576-47798626	HAEpiC	amniotic membrane:	n/a
45	chr1:47798576-47798626	BJ	skin:	n/a
46	chr1:47798576-47798626	GM06990	blood:	n/a
47	chr1:47798576-47798626	HEK293	kidney:	embryo
48	chr1:47798576-47798626	NH-A	brain:	n/a
49	chr1:47798576-47798626	HRPEpiC	eye:	n/a
50	chr1:47798576-47798626	MCF10A-Er-Src	breast:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:47778595..47781681-chr1:47798356..47800996,6	MCF-7	breast:
2	chr1:47642908..47645406-chr1:47797799..47799356,2	MCF-7	breast:
3	chr1:47772551..47781833-chr1:47797933..47806586,42	K562	blood:
4	chr1:47132421..47133961-chr1:47797739..47800236,2	K562	blood:
5	chr1:47647073..47651610-chr1:47798272..47801392,5	K562	blood:
6	chr1:47696333..47699229-chr1:47798340..47801363,4	K562	blood:

No data

Variant related genes	Relation type
CMPK1	TF binding region
CMPK1	CpG island
ENSG00000123473	Chromatin interaction
ENSG00000224805	Chromatin interaction
ENSG00000162367	Chromatin interaction
ENSG00000225506	Chromatin interaction
ENSG00000123472	Chromatin interaction
ENSG00000162366	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11211487	0.85[AMR][1000 genomes]
rs11211494	0.85[AMR][1000 genomes]
rs11211509	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11802603	0.85[AMR][1000 genomes]
rs12061032	0.85[AMR][1000 genomes]
rs12092248	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13375432	1.00[MEX][hapmap]
rs13376465	0.92[ASW][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.83[AMR][1000 genomes]
rs17103087	0.83[AMR][1000 genomes]
rs55830339	0.83[AMR][1000 genomes]
rs55833824	0.83[AMR][1000 genomes]
rs57573975	0.85[AMR][1000 genomes]
rs61243812	0.85[AMR][1000 genomes]
rs6588095	1.00[MEX][hapmap];0.93[MKK][hapmap];0.85[AMR][1000 genomes]
rs6656779	0.83[ASW][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.83[AMR][1000 genomes]
rs6660505	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6702191	0.83[AMR][1000 genomes]
rs74074045	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390574	chr1:47778981-47803091	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	esv3380025	chr1:47798390-47801238	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47792800-47798600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr1:47795600-47798600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:47796600-47798600	Enhancers	Esophagus	oesophagus
4	chr1:47797600-47799200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:47797800-47798600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:47797800-47798600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:47797800-47798600	Enhancers	Brain Anterior Caudate	brain
8	chr1:47797800-47798600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr1:47797800-47798600	Enhancers	Fetal Kidney	kidney
10	chr1:47797800-47798600	Enhancers	Fetal Muscle Leg	muscle
11	chr1:47797800-47798600	Enhancers	Fetal Stomach	stomach
12	chr1:47797800-47798600	Enhancers	Right Atrium	heart
13	chr1:47797800-47798800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:47797800-47798800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:47797800-47798800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:47797800-47799000	Flanking Active TSS	Fetal Brain Female	brain
17	chr1:47797800-47799000	Flanking Active TSS	K562	blood
18	chr1:47797800-47799200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:47797800-47799200	Enhancers	Small Intestine	intestine
20	chr1:47798000-47798600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:47798000-47798600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:47798000-47798600	Enhancers	Liver	Liver
23	chr1:47798000-47798600	Enhancers	Left Ventricle	heart
24	chr1:47798000-47798600	Enhancers	Right Ventricle	heart
25	chr1:47798000-47798600	Enhancers	HUVEC	blood vessel
26	chr1:47798000-47798600	Enhancers	NHDF-Ad	bronchial
27	chr1:47798000-47798800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:47798000-47798800	Enhancers	Placenta	Placenta
29	chr1:47798000-47798800	Enhancers	Pancreas	Pancrea
30	chr1:47798000-47798800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr1:47798000-47799000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:47798000-47799000	Enhancers	Aorta	Aorta
33	chr1:47798000-47799000	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr1:47798000-47799000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr1:47798000-47799000	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr1:47798000-47799000	Enhancers	Stomach Mucosa	stomach
37	chr1:47798000-47799000	Flanking Active TSS	HepG2	liver
38	chr1:47798000-47799200	Flanking Active TSS	Hela-S3	cervix
39	chr1:47798000-47799400	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr1:47798000-47799400	Flanking Active TSS	Dnd41	blood
41	chr1:47798200-47798600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr1:47798200-47798600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:47798200-47798600	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:47798200-47798600	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr1:47798200-47798600	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr1:47798200-47798600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:47798200-47798600	Enhancers	Adipose Nuclei	Adipose
48	chr1:47798200-47798600	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr1:47798200-47798600	Enhancers	Brain Substantia Nigra	brain
50	chr1:47798200-47798600	Enhancers	Fetal Lung	lung

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