Variant report

Variant	rs12039184
Chromosome Location	chr1:225961942-225961943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr1:225961766-225962036	Hela-S3	cervix:	n/a	n/a
2	PBX3	chr1:225961923-225962502	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr1:225961860-225962010	HEK293	kidney:	n/a	n/a
4	CTCF	chr1:225961880-225962030	HEK293	kidney:	n/a	n/a
5	REST	chr1:225961849-225962791	H1-neurons	neurons:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:225741016..225742575-chr1:225960574..225962350,2	MCF-7	breast:
2	chr1:225948046..225950619-chr1:225959798..225962169,2	MCF-7	breast:
3	chr1:225958118..225962710-chr1:225963667..225967066,7	K562	blood:
4	chr1:225907278..225910791-chr1:225959597..225963050,3	MCF-7	breast:
5	chr1:225956937..225960087-chr1:225960479..225963654,4	K562	blood:
6	chr1:225961838..225964716-chr1:226068822..226070788,2	K562	blood:
7	chr1:225960600..225963224-chr1:225967142..225968691,2	K562	blood:
8	chr1:225957183..225958827-chr1:225960049..225962643,2	MCF-7	breast:
9	chr1:225959006..225964473-chr1:225964619..225968366,9	MCF-7	breast:

No data

Variant related genes	Relation type
SRP9	TF binding region
ENSG00000196187	Chromatin interaction
ENSG00000143742	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10915869	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10915871	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10915872	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[GIH][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10915874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915875	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12021669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12021809	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12023203	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12023665	0.85[CEU][hapmap]
rs12025075	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12025085	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12025267	0.92[CEU][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12026657	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12029847	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12031637	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12032511	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12034342	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12038476	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12042000	0.83[EUR][1000 genomes]
rs12042778	0.84[EUR][1000 genomes]
rs12047520	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12048908	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12562612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1849685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1857008	0.85[CEU][hapmap]
rs2078389	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3738035	1.00[AFR][1000 genomes]
rs3753650	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4557929	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs61849043	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs61849046	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs61849047	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs61851667	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs716966	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225952200-225964400	Weak transcription	Fetal Brain Female	brain
2	chr1:225952200-225965600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:225954800-225964400	Weak transcription	Small Intestine	intestine
4	chr1:225956800-225964600	Weak transcription	Right Ventricle	heart
5	chr1:225957000-225965000	Weak transcription	Gastric	stomach
6	chr1:225957400-225962200	Enhancers	HepG2	liver
7	chr1:225958000-225962200	Enhancers	A549	lung
8	chr1:225958000-225963600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:225958200-225963400	Enhancers	HSMM	muscle
10	chr1:225958600-225962600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:225958600-225963200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:225958600-225964800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:225959200-225964600	Weak transcription	Psoas Muscle	Psoas
14	chr1:225959200-225964800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:225959600-225962400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:225959600-225962600	Enhancers	Stomach Mucosa	stomach
17	chr1:225959600-225964800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:225959600-225964800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:225959800-225964400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:225960000-225964600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:225960000-225964600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:225960200-225963200	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr1:225960200-225964200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:225960200-225964400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:225960200-225964800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr1:225960400-225962600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:225960400-225962800	Enhancers	Stomach Smooth Muscle	stomach
28	chr1:225960400-225963200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:225960400-225963800	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr1:225960400-225964200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr1:225960400-225964400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:225960400-225964400	Weak transcription	Primary B cells from peripheral blood	blood
33	chr1:225960400-225964400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr1:225960400-225964400	Weak transcription	Brain Substantia Nigra	brain
35	chr1:225960400-225964400	Weak transcription	Fetal Muscle Leg	muscle
36	chr1:225960400-225964400	Weak transcription	HUVEC	blood vessel
37	chr1:225960400-225964400	Weak transcription	NHDF-Ad	bronchial
38	chr1:225960400-225964600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:225960400-225965000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:225960600-225963200	Enhancers	HSMMtube	muscle
41	chr1:225960600-225964200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr1:225960600-225964400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:225960600-225964600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:225960600-225964600	Weak transcription	Fetal Brain Male	brain
45	chr1:225960600-225964600	Weak transcription	Fetal Heart	heart
46	chr1:225960600-225964800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:225960800-225962000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr1:225960800-225962000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:225960800-225962000	Enhancers	Fetal Lung	lung
50	chr1:225960800-225964000	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links