Variant report

Variant	rs12503961
Chromosome Location	chr4:2942759-2942760
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:2907975..2910281-chr4:2941881..2943677,2	MCF-7	breast:
2	chr4:2790052..2809152-chr4:2930639..2948075,83	MCF-7	breast:
3	chr4:2941284..2943346-chr4:2963790..2966270,3	MCF-7	breast:
4	chr4:2940357..2942863-chr4:2954214..2956464,2	K562	blood:
5	chr11:62609089..62610637-chr4:2941968..2944079,2	MCF-7	breast:
6	chr4:2798770..2801758-chr4:2941180..2943976,2	K562	blood:
7	chr4:2906552..2911481-chr4:2934891..2942965,11	MCF-7	breast:
8	chr4:2844829..2846512-chr4:2941018..2943974,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADD1-1	chr4:2942029-2943596	ENSG00000249673
2	lnc-ADD1-1	chr4:2942029-2943778	ENSG00000249673.2

No data

Variant related genes	Relation type
ENSG00000125388	Chromatin interaction
ENSG00000087266	Chromatin interaction
ENSG00000087274	Chromatin interaction
ENSG00000087269	Chromatin interaction
ENSG00000133316	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1063744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506119	0.83[CHD][hapmap]
rs12511823	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13103004	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13111777	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs1419043	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs7665452	1.00[ASW][hapmap];0.89[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7667661	1.00[ASW][hapmap];0.89[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	esv3375632	chr4:2941604-2944102	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv3464673	chr4:2942602-2942877	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3464671	chr4:2942635-2942904	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3464672	chr4:2942669-2942840	Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv3464674	chr4:2942683-2942839	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	6 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	chr4:2937800-2945800	Weak transcription	Fetal Kidney	kidney
2	chr4:2938000-2945400	Genic enhancers	Primary T cells fromperipheralblood	blood
3	chr4:2938000-2960400	Weak transcription	Right Atrium	heart
4	chr4:2938200-2946800	Strong transcription	Thymus	Thymus
5	chr4:2938200-2948400	Strong transcription	Fetal Intestine Small	intestine
6	chr4:2938200-2962200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:2938400-2944400	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:2938400-2957600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:2938400-2959600	Strong transcription	Brain Anterior Caudate	brain
10	chr4:2938400-2962200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr4:2938600-2943800	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr4:2938600-2949600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr4:2938600-2960400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:2938600-2960400	Strong transcription	Brain Cingulate Gyrus	brain
15	chr4:2938600-2961000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:2938600-2961600	Strong transcription	Primary T cells from cord blood	blood
17	chr4:2938600-2961600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:2938800-2944000	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr4:2938800-2955600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:2938800-2956800	Strong transcription	Fetal Intestine Large	intestine
21	chr4:2938800-2959200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:2938800-2961000	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr4:2938800-2961000	Strong transcription	Primary hematopoietic stem cells	blood
24	chr4:2938800-2961000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:2939000-2943000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr4:2939000-2956800	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr4:2939000-2956800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr4:2939000-2957400	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:2939000-2958400	Strong transcription	Brain Substantia Nigra	brain
30	chr4:2939000-2960200	Strong transcription	Lung	lung
31	chr4:2939000-2961600	Strong transcription	Fetal Stomach	stomach
32	chr4:2939200-2953800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:2939200-2956200	Strong transcription	Left Ventricle	heart
34	chr4:2939200-2959200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:2939200-2959600	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr4:2939200-2960000	Strong transcription	Stomach Smooth Muscle	stomach
37	chr4:2939200-2960600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr4:2939200-2961000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr4:2939200-2963200	Weak transcription	Fetal Heart	heart
40	chr4:2939400-2944200	Strong transcription	Duodenum Mucosa	Duodenum
41	chr4:2939400-2945800	Strong transcription	HSMMtube	muscle
42	chr4:2939400-2948000	Strong transcription	Liver	Liver
43	chr4:2939400-2952600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:2939400-2956800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:2939400-2957200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:2939400-2959000	Strong transcription	Ovary	ovary
47	chr4:2939400-2959400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr4:2939400-2959600	Strong transcription	Adipose Nuclei	Adipose
49	chr4:2939400-2959600	Strong transcription	HUVEC	blood vessel
50	chr4:2939400-2959800	Strong transcription	Fetal Muscle Leg	muscle

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