Variant report

Variant	rs4244629
Chromosome Location	chr1:246949691-246949692
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:246948383-246949809	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:246941244..246944008-chr1:246946969..246949951,3	MCF-7	breast:
2	chr1:246944573..246947572-chr1:246947936..246950947,5	K562	blood:
3	chr1:246947863..246950737-chr1:246955534..246958026,3	K562	blood:
4	chr1:246945490..246947572-chr1:246949447..246951570,2	K562	blood:
5	chr1:246939030..246940776-chr1:246947263..246949787,2	MCF-7	breast:
6	chr1:246947185..246952305-chr1:246952338..246955724,5	K562	blood:

No data

Variant related genes	Relation type
KIF28P	TF binding region
ENSG00000227953	TF binding region
ENSG00000223519	Chromatin interaction
ENSG00000227953	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10732299	1.00[AMR][1000 genomes]
rs10924822	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12040914	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12069175	1.00[AMR][1000 genomes]
rs12071299	1.00[AMR][1000 genomes]
rs1691257	1.00[AMR][1000 genomes]
rs1779973	1.00[AMR][1000 genomes]
rs1779976	1.00[AMR][1000 genomes]
rs2800223	1.00[AMR][1000 genomes]
rs2996552	1.00[AMR][1000 genomes]
rs3007320	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3007321	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3007325	1.00[AMR][1000 genomes]
rs3007326	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3007327	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3122533	1.00[AMR][1000 genomes]
rs4244625	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4244626	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4244631	1.00[AFR][1000 genomes]
rs4511163	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4532864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4926452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4926463	1.00[AMR][1000 genomes]
rs6426335	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6663093	1.00[AMR][1000 genomes]
rs6696798	1.00[AMR][1000 genomes]
rs7416659	1.00[AMR][1000 genomes]
rs923972	1.00[AMR][1000 genomes]
rs9426266	1.00[AMR][1000 genomes]
rs9426274	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv1006262	chr1:246892826-246964775	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv523531	chr1:246893948-246967899	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv999756	chr1:246894542-246969660	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv1009436	chr1:246910373-246965832	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv873423	chr1:246923861-246978504	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
14	nsv549545	chr1:246936353-246963019	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	esv1841827	chr1:246944502-246954313	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246902800-246952800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:246925200-246952200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:246932400-246952000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:246932800-246952400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:246932800-246956400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:246940800-246951600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:246940800-246951600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:246941200-246952600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:246941600-246952200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:246942800-246952200	Weak transcription	Fetal Brain Female	brain
11	chr1:246943400-246952000	Weak transcription	Brain Anterior Caudate	brain
12	chr1:246944600-246952200	Weak transcription	NH-A	brain
13	chr1:246944800-246952000	Weak transcription	Fetal Intestine Large	intestine
14	chr1:246944800-246952200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:246945800-246956400	Weak transcription	A549	lung
16	chr1:246946200-246952200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:246946200-246952400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:246946200-246956800	Weak transcription	Left Ventricle	heart
19	chr1:246947200-246952200	Weak transcription	Fetal Intestine Small	intestine
20	chr1:246948000-246952200	Weak transcription	Right Atrium	heart
21	chr1:246948400-246952200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:246948600-246950400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:246948800-246951200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:246948800-246952200	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:246949000-246950000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:246949000-246951400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:246949000-246952000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:246949000-246952000	Weak transcription	GM12878-XiMat	blood
29	chr1:246949000-246952400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:246949000-246957600	Weak transcription	NHDF-Ad	bronchial
31	chr1:246949200-246950400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:246949200-246951000	Weak transcription	Liver	Liver
33	chr1:246949200-246951200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:246949200-246951400	Weak transcription	Placenta	Placenta
35	chr1:246949200-246952000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr1:246949200-246952000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr1:246949200-246952200	Weak transcription	Brain Angular Gyrus	brain
38	chr1:246949200-246952200	Weak transcription	Colon Smooth Muscle	Colon
39	chr1:246949200-246952200	Weak transcription	Right Ventricle	heart
40	chr1:246949200-246952800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:246949200-246952800	Weak transcription	Spleen	Spleen
42	chr1:246949200-246953000	Weak transcription	Gastric	stomach
43	chr1:246949400-246949800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr1:246949400-246949800	Weak transcription	Fetal Muscle Leg	muscle
45	chr1:246949400-246950200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:246949400-246951200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:246949400-246951200	Weak transcription	Fetal Stomach	stomach
48	chr1:246949400-246952000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:246949400-246952000	Weak transcription	Fetal Heart	heart
50	chr1:246949400-246952000	Weak transcription	Fetal Lung	lung

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