Variant report

Variant	rs104902
Chromosome Location	chr3:52230440-52230441
allele	A/C
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	MYC	chr3:52229974-52230444	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52230218..52232025-chr3:52253839..52255688,2	K562	blood:
2	chr3:52028577..52031266-chr3:52230149..52233019,2	K562	blood:
3	chr3:52230039..52234196-chr3:52236127..52242387,6	K562	blood:
4	chr3:52087390..52089445-chr3:52228138..52231082,2	K562	blood:

Variant related genes	Relation type
ALAS1	TF binding region
ENSG00000023330	Chromatin interaction
ENSG00000162244	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs13065677	0.84[ASN][1000 genomes]
rs13071708	0.84[ASN][1000 genomes]
rs13093555	0.92[ASN][1000 genomes]
rs13098856	0.84[ASN][1000 genomes]
rs164636	0.84[ASN][1000 genomes]
rs164637	0.84[ASN][1000 genomes]
rs164641	0.84[ASN][1000 genomes]
rs34385735	0.84[ASN][1000 genomes]
rs34551211	0.92[ASN][1000 genomes]
rs35130772	0.84[ASN][1000 genomes]
rs352141	0.92[ASN][1000 genomes]
rs352155	0.82[EUR][1000 genomes]
rs352156	0.85[EUR][1000 genomes]
rs352159	0.91[EUR][1000 genomes]
rs352160	0.91[EUR][1000 genomes]
rs352173	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs353545	0.92[ASN][1000 genomes]
rs353548	0.84[ASN][1000 genomes]
rs3796342	0.84[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	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
5	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
8	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
9	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52217600-52231600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52222200-52231600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr3:52224600-52230800	Weak transcription	Psoas Muscle	Psoas
4	chr3:52224800-52231400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:52225000-52231400	Weak transcription	NH-A	brain
6	chr3:52225400-52231200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:52225400-52231200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:52225400-52231200	Weak transcription	Pancreas	Pancrea
9	chr3:52225400-52231200	Weak transcription	Right Atrium	heart
10	chr3:52225800-52231200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:52226600-52231600	Enhancers	Placenta	Placenta
12	chr3:52226800-52231600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:52226800-52232000	Enhancers	Spleen	Spleen
14	chr3:52227400-52230800	Weak transcription	Gastric	stomach
15	chr3:52227400-52231400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:52227400-52231600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:52227400-52231600	Enhancers	Fetal Muscle Trunk	muscle
18	chr3:52227600-52230800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:52227600-52230800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:52227600-52230800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:52227600-52230800	Weak transcription	A549	lung
22	chr3:52227600-52231000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:52227600-52231000	Weak transcription	Brain Angular Gyrus	brain
24	chr3:52227600-52231000	Weak transcription	Brain Anterior Caudate	brain
25	chr3:52227600-52231000	Weak transcription	Esophagus	oesophagus
26	chr3:52227600-52231000	Weak transcription	HSMM	muscle
27	chr3:52227600-52231000	Weak transcription	HSMMtube	muscle
28	chr3:52227600-52231200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr3:52227800-52230800	Weak transcription	Brain Hippocampus Middle	brain
30	chr3:52228200-52231000	Weak transcription	Brain Substantia Nigra	brain
31	chr3:52228200-52231400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:52228200-52231600	Enhancers	Fetal Intestine Small	intestine
33	chr3:52228200-52231600	Enhancers	Fetal Stomach	stomach
34	chr3:52228400-52231200	Enhancers	Colonic Mucosa	Colon
35	chr3:52228600-52231200	Weak transcription	Fetal Kidney	kidney
36	chr3:52228600-52231200	Enhancers	Stomach Smooth Muscle	stomach
37	chr3:52228800-52230800	Weak transcription	Fetal Thymus	thymus
38	chr3:52229000-52230800	Enhancers	Stomach Mucosa	stomach
39	chr3:52229000-52231200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr3:52229000-52231600	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr3:52229200-52231400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:52229200-52231400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:52229200-52231600	Enhancers	K562	blood
44	chr3:52229200-52231800	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr3:52229400-52230800	Enhancers	Duodenum Mucosa	Duodenum
46	chr3:52229400-52231000	Weak transcription	Fetal Heart	heart
47	chr3:52229400-52231200	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr3:52229400-52231400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:52229400-52231400	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr3:52229400-52231600	Enhancers	Primary B cells from cord blood	blood

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