Variant report

Variant	rs2229648
Chromosome Location	chr3:50325638-50325639
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50296030..50318456-chr3:50318822..50339499,66	MCF-7	breast:
2	chr3:50324564..50342616-chr3:50350801..50362499,49	MCF-7	breast:
3	chr3:50311065..50313407-chr3:50322808..50325797,2	MCF-7	breast:
4	chr3:50309059..50311667-chr3:50323698..50326427,2	K562	blood:
5	chr3:50325622..50330493-chr3:50373581..50377874,6	K562	blood:

Variant related genes	Relation type
ENSG00000179564	Chromatin interaction
ENSG00000068028	Chromatin interaction
ENSG00000230454	Chromatin interaction
ENSG00000232352	Chromatin interaction
ENSG00000012171	Chromatin interaction
ENSG00000068001	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12107362	1.00[AMR][1000 genomes]
rs12107386	1.00[AMR][1000 genomes]
rs17050905	1.00[AMR][1000 genomes]
rs17050921	1.00[AMR][1000 genomes]
rs17050924	1.00[AMR][1000 genomes]
rs17849464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2233477	1.00[AMR][1000 genomes]
rs55913179	1.00[AMR][1000 genomes]
rs56297242	1.00[AMR][1000 genomes]
rs58095278	1.00[AMR][1000 genomes]
rs58363428	1.00[AMR][1000 genomes]
rs58418366	1.00[AMR][1000 genomes]
rs59822920	1.00[AMR][1000 genomes]
rs60065407	1.00[AMR][1000 genomes]
rs73832789	1.00[AMR][1000 genomes]
rs73832800	1.00[AMR][1000 genomes]
rs73832801	1.00[AMR][1000 genomes]
rs73833385	1.00[AMR][1000 genomes]
rs73835208	1.00[AMR][1000 genomes]
rs73835216	1.00[AMR][1000 genomes]
rs73835217	1.00[AMR][1000 genomes]
rs73835235	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835504	1.00[AMR][1000 genomes]
rs73835507	1.00[AMR][1000 genomes]
rs73835518	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv590250	chr3:50153356-50332697	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
6	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
7	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
8	nsv590251	chr3:50158774-50337422	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
10	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
11	nsv523560	chr3:50172397-50339163	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
12	nsv1014256	chr3:50187646-50339163	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
13	nsv536565	chr3:50187646-50339163	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
14	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
15	nsv590253	chr3:50196418-50337422	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
16	esv2757870	chr3:50198478-50371377	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
17	esv2759148	chr3:50198478-50371377	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
18	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
19	nsv590254	chr3:50243510-50388607	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
20	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
21	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
22	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
23	nsv590257	chr3:50302830-50393640	Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
24	nsv590256	chr3:50302830-50420554	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
25	nsv876774	chr3:50302830-50436827	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
26	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
27	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
28	esv3398486	chr3:50322998-50325696	Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
29	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2229648	ENSG00000214706	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50310800-50325800	Weak transcription	HSMM	muscle
2	chr3:50320600-50327400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:50321000-50328400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:50322800-50327800	Strong transcription	Fetal Intestine Small	intestine
5	chr3:50322800-50328000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:50322800-50328600	Weak transcription	Small Intestine	intestine
7	chr3:50323000-50326000	Weak transcription	Stomach Mucosa	stomach
8	chr3:50323200-50327800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:50323200-50327800	Weak transcription	GM12878-XiMat	blood
10	chr3:50323200-50328000	Strong transcription	A549	lung
11	chr3:50323200-50328400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:50323400-50327400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:50323400-50327400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:50323400-50327400	Strong transcription	Brain Germinal Matrix	brain
15	chr3:50323400-50327400	Strong transcription	Dnd41	blood
16	chr3:50323400-50327600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:50323400-50327600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:50323400-50327800	Strong transcription	Fetal Thymus	thymus
19	chr3:50323400-50328000	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr3:50323400-50328000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:50323400-50328000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:50323400-50328000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:50323400-50328000	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr3:50323400-50328000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:50323400-50328000	Strong transcription	Lung	lung
26	chr3:50323400-50328000	Strong transcription	Thymus	Thymus
27	chr3:50323400-50328200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:50323400-50328200	Strong transcription	Fetal Muscle Leg	muscle
29	chr3:50323400-50328200	Genic enhancers	Right Ventricle	heart
30	chr3:50323400-50328400	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:50323600-50327200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr3:50323600-50327600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:50323600-50327600	Strong transcription	Brain Anterior Caudate	brain
34	chr3:50323600-50327800	Strong transcription	Primary T cells from cord blood	blood
35	chr3:50323600-50328000	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:50323600-50328200	Strong transcription	Fetal Brain Female	brain
37	chr3:50323600-50328200	Strong transcription	Placenta	Placenta
38	chr3:50323800-50325800	Genic enhancers	Left Ventricle	heart
39	chr3:50323800-50327200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:50323800-50327600	Strong transcription	Spleen	Spleen
41	chr3:50323800-50327800	Strong transcription	Stomach Smooth Muscle	stomach
42	chr3:50323800-50328000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:50323800-50328000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr3:50323800-50328000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:50323800-50328000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:50323800-50328000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:50323800-50328000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:50323800-50328000	Strong transcription	Brain Angular Gyrus	brain
49	chr3:50323800-50328000	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:50323800-50328000	Strong transcription	NHEK	skin

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