Variant report

Variant	rs12144608
Chromosome Location	chr1:246948478-246948479
allele	C/T
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	POLR2A	chr1:246948472-246948495	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:246948383-246949809	HepG2	liver:	n/a	n/a
3	ELF1	chr1:246948213-246948519	K562	blood:	n/a	chr1:246948354-246948367 chr1:246948357-246948366 chr1:246948315-246948324
4	MYC	chr1:246947843-246948764	NB4	blood:	n/a	chr1:246948130-246948140 chr1:246948123-246948139
5	POLR2A	chr1:246948237-246948534	HUVEC	blood vessel:	n/a	n/a
6	MAX	chr1:246947918-246948800	NB4	blood:	n/a	chr1:246948130-246948140 chr1:246948123-246948139
7	MAX	chr1:246948446-246948687	K562	blood:	n/a	n/a

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	chr1:246939030..246940776-chr1:246947263..246949787,2	MCF-7	breast:
5	chr1:246946643..246948588-chr1:247104112..247106785,2	K562	blood:
6	chr1:246947185..246952305-chr1:246952338..246955724,5	K562	blood:

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

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10924821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12117138	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12123234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12124249	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12129922	1.00[AMR][1000 genomes]
rs12136007	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12143299	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35650616	1.00[AFR][1000 genomes]
rs57538659	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61852473	1.00[AMR][1000 genomes]
rs61852483	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61852486	1.00[AMR][1000 genomes]
rs61852487	0.88[EUR][1000 genomes]
rs61852488	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61852489	0.88[EUR][1000 genomes]
rs61852490	0.88[EUR][1000 genomes]
rs61852513	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61852517	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6665017	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6676751	0.88[EUR][1000 genomes]
rs74154805	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	esv3408268	chr1:246944429-246948627	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	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:94 , 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	chr1:246932600-246948600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:246932600-246948600	Weak transcription	Esophagus	oesophagus
6	chr1:246932800-246948800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:246932800-246952400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:246932800-246956400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:246940200-246948800	Weak transcription	Fetal Brain Male	brain
10	chr1:246940400-246949000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:246940600-246948600	Weak transcription	Brain Angular Gyrus	brain
12	chr1:246940600-246948800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:246940600-246948800	Weak transcription	Fetal Kidney	kidney
14	chr1:246940800-246951600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:246940800-246951600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:246941200-246952600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:246941600-246948800	Weak transcription	Colonic Mucosa	Colon
18	chr1:246941600-246948800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:246941600-246952200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:246942200-246949000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:246942800-246952200	Weak transcription	Fetal Brain Female	brain
22	chr1:246943400-246952000	Weak transcription	Brain Anterior Caudate	brain
23	chr1:246944400-246948800	Weak transcription	Gastric	stomach
24	chr1:246944600-246952200	Weak transcription	NH-A	brain
25	chr1:246944800-246952000	Weak transcription	Fetal Intestine Large	intestine
26	chr1:246944800-246952200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:246945000-246948800	Weak transcription	Brain Germinal Matrix	brain
28	chr1:246945200-246949400	Enhancers	Fetal Muscle Leg	muscle
29	chr1:246945800-246949000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr1:246945800-246956400	Weak transcription	A549	lung
31	chr1:246946000-246948800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr1:246946200-246948600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:246946200-246948600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:246946200-246948600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:246946200-246948800	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:246946200-246948800	Weak transcription	Right Ventricle	heart
37	chr1:246946200-246952200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:246946200-246952400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr1:246946200-246956800	Weak transcription	Left Ventricle	heart
40	chr1:246946400-246948600	Strong transcription	Fetal Stomach	stomach
41	chr1:246946400-246948800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:246947200-246948800	Weak transcription	Fetal Lung	lung
43	chr1:246947200-246952200	Weak transcription	Fetal Intestine Small	intestine
44	chr1:246947400-246949200	Enhancers	HSMMtube	muscle
45	chr1:246947600-246948600	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr1:246947600-246948600	Enhancers	Primary B cells from peripheral blood	blood
47	chr1:246947600-246948800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:246947800-246948600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:246947800-246948600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr1:246947800-246948800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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