Variant report

Variant	rs61046241
Chromosome Location	chr1:46090538-46090539
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:46085707-46090542	K562	blood:	n/a	n/a
2	POLR2A	chr1:46082631-46090552	K562	blood:	n/a	n/a
3	POLR2A	chr1:46088530-46090808	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:46080556-46090554	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:46090494-46090544	HEK293	kidney:	embryo
2	chr1:46090494-46090544	MCF10A-Er-Src	breast:	n/a
3	chr1:46090494-46090544	BE2_C	brain:	n/a
4	chr1:46090494-46090544	NB4	blood:	n/a
5	chr1:46090494-46090544	HRPEpiC	eye:	n/a
6	chr1:46090494-46090544	HUVEC	blood vessel:	n/a
7	chr1:46090494-46090544	HMEC	breast:	n/a
8	chr1:46090494-46090544	BJ	skin:	n/a
9	chr1:46090494-46090544	Jurkat	blood:	n/a
10	chr1:46090494-46090544	GM06990	blood:	n/a
11	chr1:46090494-46090544	H1-hESC	embryonic stem cell:	embryo
12	chr1:46090494-46090544	HIPEpiC	eye:	n/a
13	chr1:46090494-46090544	A549	lung:	n/a
14	chr1:46090494-46090544	NHBE	bronchial:	n/a
15	chr1:46090494-46090544	AG09309	skin:	n/a
16	chr1:46090494-46090544	HNPCEpiC	eye:	n/a
17	chr1:46090494-46090544	PrEC	prostate:	n/a
18	chr1:46090494-46090544	HPAEpiC	pulmonary alveolar:	n/a
19	chr1:46090494-46090544	Caco-2	colon:	n/a
20	chr1:46090494-46090544	HL-60	blood:	n/a
21	chr1:46090494-46090544	HepG2	liver:	n/a
22	chr1:46090494-46090544	HRE	kidney:	n/a
23	chr1:46090494-46090544	HCF	heart:	n/a
24	chr1:46090494-46090544	GM12892	blood:	n/a
25	chr1:46090494-46090544	AG04450	lung:	fetal
26	chr1:46090494-46090544	GM12878	blood:	n/a
27	chr1:46090494-46090544	NHDF-neo	bronchial:	n/a
28	chr1:46090494-46090544	LNCaP	prostate:	n/a
29	chr1:46090494-46090544	ProgFib	skin:	n/a
30	chr1:46090494-46090544	SAEC	small airway:	n/a
31	chr1:46090494-46090544	NT2-D1	testis:	n/a
32	chr1:46090494-46090544	SK-N-MC	brain:	n/a
33	chr1:46090494-46090544	AG10803	skin:	n/a
34	chr1:46090494-46090544	PANC-1	pancreas:	n/a
35	chr1:46090494-46090544	ECC-1	luminal epithelium:	n/a
36	chr1:46090494-46090544	K562	blood:	n/a
37	chr1:46090494-46090544	HRCEpiC	kidney:	n/a
38	chr1:46090494-46090544	Hela-S3	cervix:	n/a
39	chr1:46090494-46090544	HCPEpiC	choroid plexus:	n/a
40	chr1:46090494-46090544	T-47D	breast:	n/a
41	chr1:46090494-46090544	RPTEC	kidney:	n/a
42	chr1:46090494-46090544	PFSK-1	brain:	n/a
43	chr1:46090494-46090544	IMR90	lung:	fetal
44	chr1:46090494-46090544	NH-A	brain:	n/a
45	chr1:46090494-46090544	Hepatocyte	liver:	n/a
46	chr1:46090494-46090544	SKMC	muscle:	n/a
47	chr1:46090494-46090544	SK-N-SH_RA	brain:	n/a
48	chr1:46090494-46090544	SK-N-SH	brain:	n/a
49	chr1:46090494-46090544	ovcar-3	ovarian:	n/a
50	chr1:46090494-46090544	AoSMC	blood vessel:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:46088002..46091701-chr1:46094509..46096362,4	K562	blood:
2	chr1:46048860..46051215-chr1:46089890..46092822,3	K562	blood:
3	chr1:46048178..46050215-chr1:46089233..46091590,2	K562	blood:

No data

Variant related genes	Relation type
CCDC17	TF binding region
CCDC17	CpG island
ENSG00000132780	Chromatin interaction
ENSG00000159592	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs55642657	1.00[AMR][1000 genomes]
rs55958907	1.00[AMR][1000 genomes]
rs72889328	1.00[AMR][1000 genomes]
rs72891030	1.00[AMR][1000 genomes]
rs74072078	1.00[AFR][1000 genomes];1.00[AMR][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	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
2	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
3	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
4	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
5	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
6	nsv1011587	chr1:46051672-46244492	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46052800-46099400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:46053200-46127400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:46070000-46108200	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:46071200-46093000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:46071600-46105800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:46074800-46108200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:46076200-46094000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:46077800-46112600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr1:46078200-46101200	Strong transcription	Thymus	Thymus
10	chr1:46078400-46100800	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:46078800-46101000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:46079000-46100600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:46079600-46094600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:46079800-46109800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:46082000-46090800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:46083200-46093000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:46083200-46094000	Weak transcription	Small Intestine	intestine
18	chr1:46083400-46095000	Weak transcription	Stomach Mucosa	stomach
19	chr1:46083600-46091400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr1:46083600-46091800	Weak transcription	Brain Substantia Nigra	brain
21	chr1:46083600-46093800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:46083800-46092400	Weak transcription	NHDF-Ad	bronchial
23	chr1:46083800-46093600	Weak transcription	Aorta	Aorta
24	chr1:46084000-46093600	Weak transcription	Fetal Brain Male	brain
25	chr1:46084200-46093200	Weak transcription	Hela-S3	cervix
26	chr1:46084200-46093600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:46084200-46093600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:46084400-46091200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:46084400-46091400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:46084400-46091400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:46084400-46093600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:46084400-46094800	Weak transcription	Fetal Kidney	kidney
33	chr1:46084600-46092800	Weak transcription	NH-A	brain
34	chr1:46085000-46091400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:46085000-46091600	Weak transcription	Brain Angular Gyrus	brain
36	chr1:46085200-46093600	Weak transcription	Psoas Muscle	Psoas
37	chr1:46085400-46091400	Weak transcription	HMEC	breast
38	chr1:46085800-46091400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr1:46085800-46093400	Weak transcription	HepG2	liver
40	chr1:46086000-46096000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr1:46086400-46091400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:46086600-46091200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:46087000-46091400	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr1:46087400-46091400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr1:46087600-46129200	Strong transcription	Fetal Thymus	thymus
46	chr1:46088000-46094400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:46088200-46095200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:46088200-46110000	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr1:46088400-46091800	Weak transcription	Fetal Lung	lung
50	chr1:46088400-46093400	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links