Variant report

Variant	rs6426133
Chromosome Location	chr1:224698363-224698364
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:224698362-224698412	HIPEpiC	eye:	n/a
2	chr1:224698362-224698412	GM12891	blood:	n/a
3	chr1:224698362-224698412	SAEC	small airway:	n/a
4	chr1:224698362-224698412	HRCEpiC	kidney:	n/a
5	chr1:224698362-224698412	Caco-2	colon:	n/a
6	chr1:224698362-224698412	HNPCEpiC	eye:	n/a
7	chr1:224698362-224698412	HL-60	blood:	n/a
8	chr1:224698362-224698412	U87	brain:	n/a
9	chr1:224698362-224698412	Jurkat	blood:	n/a
10	chr1:224698362-224698412	HCPEpiC	choroid plexus:	n/a
11	chr1:224698362-224698412	IMR90	lung:	fetal
12	chr1:224698362-224698412	PANC-1	pancreas:	n/a
13	chr1:224698362-224698412	SK-N-SH_RA	brain:	n/a
14	chr1:224698362-224698412	NHDF-neo	bronchial:	n/a
15	chr1:224698362-224698412	AG04449	skin:	fetal
16	chr1:224698362-224698412	HepG2	liver:	n/a
17	chr1:224698362-224698412	HCM	heart:	n/a
18	chr1:224698362-224698412	Hepatocyte	liver:	n/a
19	chr1:224698362-224698412	K562	blood:	n/a
20	chr1:224698362-224698412	BE2_C	brain:	n/a
21	chr1:224698362-224698412	NB4	blood:	n/a
22	chr1:224698362-224698412	AoSMC	blood vessel:	n/a
23	chr1:224698362-224698412	HPAEpiC	pulmonary alveolar:	n/a
24	chr1:224698362-224698412	SKMC	muscle:	n/a
25	chr1:224698362-224698412	HRE	kidney:	n/a
26	chr1:224698362-224698412	AG09319	gingival:	n/a
27	chr1:224698362-224698412	PFSK-1	brain:	n/a
28	chr1:224698362-224698412	T-47D	breast:	n/a
29	chr1:224698362-224698412	AG09309	skin:	n/a
30	chr1:224698362-224698412	HEEpiC	esophagus:	n/a
31	chr1:224698362-224698412	HAEpiC	amniotic membrane:	n/a
32	chr1:224698362-224698412	ECC-1	luminal epithelium:	n/a
33	chr1:224698362-224698412	ovcar-3	ovarian:	n/a
34	chr1:224698362-224698412	PrEC	prostate:	n/a
35	chr1:224698362-224698412	SK-N-SH	brain:	n/a
36	chr1:224698362-224698412	HMEC	breast:	n/a
37	chr1:224698362-224698412	Hela-S3	cervix:	n/a
38	chr1:224698362-224698412	H1-hESC	embryonic stem cell:	embryo
39	chr1:224698362-224698412	HCT-116	colon:	n/a
40	chr1:224698362-224698412	ProgFib	skin:	n/a
41	chr1:224698362-224698412	HEK293	kidney:	embryo
42	chr1:224698362-224698412	MCF10A-Er-Src	breast:	n/a
43	chr1:224698362-224698412	CMK	blood:	n/a
44	chr1:224698362-224698412	NT2-D1	testis:	n/a
45	chr1:224698362-224698412	SK-N-MC	brain:	n/a
46	chr1:224698362-224698412	NHBE	bronchial:	n/a
47	chr1:224698362-224698412	AG04450	lung:	fetal
48	chr1:224698362-224698412	MCF-7	breast:	n/a
49	chr1:224698362-224698412	LNCaP	prostate:	n/a
50	chr1:224698362-224698412	RPTEC	kidney:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224696655..224698863-chr1:224699911..224701908,2	K562	blood:
2	chr1:224693369..224695979-chr1:224697952..224700518,2	K562	blood:

No data

Variant related genes	Relation type
CNIH3	CpG island
ENSG00000143786	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10753474	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10916626	0.80[ASN][1000 genomes]
rs10916628	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10916629	0.87[EUR][1000 genomes]
rs10916630	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10916631	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10916632	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12093242	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12140117	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140906	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12141016	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141708	0.91[EUR][1000 genomes]
rs12142949	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12566578	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1891243	0.81[ASN][1000 genomes]
rs1891244	0.94[EUR][1000 genomes]
rs2648743	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3738367	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4653589	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59319739	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61825792	0.94[EUR][1000 genomes]
rs6665956	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6688146	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6695773	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6699035	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs712065	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs712066	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541723	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7541917	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7545252	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7550648	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs791504	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][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	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224690000-224699400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:224690000-224702000	Enhancers	Liver	Liver
3	chr1:224691800-224698400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:224692000-224698400	Weak transcription	HSMM	muscle
5	chr1:224692000-224698400	Weak transcription	HSMMtube	muscle
6	chr1:224692000-224701600	Weak transcription	Fetal Lung	lung
7	chr1:224692400-224701600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:224692600-224698800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:224692600-224700600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:224693000-224698400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:224693600-224699200	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr1:224694200-224704000	Weak transcription	Right Atrium	heart
13	chr1:224694200-224717600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:224694200-224727600	Weak transcription	Brain Anterior Caudate	brain
15	chr1:224694400-224698400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:224694400-224698400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:224695200-224698600	Enhancers	Fetal Intestine Large	intestine
18	chr1:224695200-224699000	Enhancers	NHDF-Ad	bronchial
19	chr1:224695800-224698400	Weak transcription	HMEC	breast
20	chr1:224696400-224701200	Weak transcription	Fetal Kidney	kidney
21	chr1:224696400-224716600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:224697000-224698400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:224697000-224698600	Enhancers	Adipose Nuclei	Adipose
24	chr1:224697000-224698600	Enhancers	Colonic Mucosa	Colon
25	chr1:224697000-224699000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr1:224697000-224699000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:224697000-224699200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:224697000-224699400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:224697000-224699400	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr1:224697000-224700000	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr1:224697200-224698400	Enhancers	Stomach Mucosa	stomach
32	chr1:224697200-224698600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr1:224697200-224699200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:224697200-224699200	Enhancers	Fetal Intestine Small	intestine
35	chr1:224697200-224699200	Enhancers	K562	blood
36	chr1:224697200-224699200	Enhancers	NHEK	skin
37	chr1:224697200-224699400	Enhancers	Fetal Thymus	thymus
38	chr1:224697200-224699400	Enhancers	NHLF	lung
39	chr1:224697200-224699600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:224697200-224702200	Enhancers	Dnd41	blood
41	chr1:224697400-224698400	Weak transcription	GM12878-XiMat	blood
42	chr1:224697400-224698600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:224697400-224698600	Flanking Active TSS	HepG2	liver
44	chr1:224697400-224699000	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr1:224697400-224699200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:224697400-224699200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:224697600-224698400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:224697600-224698400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:224697600-224699200	Enhancers	NH-A	brain
50	chr1:224697800-224698600	Enhancers	Esophagus	oesophagus

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