Variant report

Variant	rs2302421
Chromosome Location	chr19:44118353-44118354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44097500..44104541-chr19:44116930..44130620,31	K562	blood:
2	chr19:44116910..44119168-chr21:47876840..47878656,2	MCF-7	breast:
3	chr19:44099462..44101775-chr19:44116930..44118818,2	K562	blood:
4	chr19:44117733..44120449-chr19:44124139..44126144,3	MCF-7	breast:
5	chr19:44117951..44120824-chr19:44143762..44146509,2	MCF-7	breast:
6	chr19:44114067..44118275-chr19:44118353..44122607,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124444	Chromatin interaction
ENSG00000167378	Chromatin interaction
ENSG00000226763	Chromatin interaction
ENSG00000105767	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11083712	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11671645	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12461175	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1402325	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1402326	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17655484	0.84[YRI][hapmap]
rs17655574	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1879387	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2003098	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2079646	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3213266	0.81[LWK][hapmap];0.80[MEX][hapmap];0.84[YRI][hapmap]
rs3213328	0.84[YRI][hapmap]
rs3746002	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3746003	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3815422	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803643	0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4803644	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73038867	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs767540	1.00[CEU][hapmap];0.84[GIH][hapmap];0.93[MEX][hapmap];0.82[EUR][1000 genomes]
rs880108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs939461	0.81[LWK][hapmap];0.80[MEX][hapmap];0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	62 gene(s)	inside rSNPs	diseases
2	nsv833839	chr19:44099813-44272299	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2302421	IZUMO2	cis	parietal	SCAN
rs2302421	ZNF615	cis	cerebellum	SCAN
rs2302421	ZNF480	cis	parietal	SCAN
rs2302421	PRRG2	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44101800-44123200	Weak transcription	Small Intestine	intestine
2	chr19:44102000-44122600	Weak transcription	Fetal Kidney	kidney
3	chr19:44102200-44122600	Weak transcription	Psoas Muscle	Psoas
4	chr19:44102400-44119600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr19:44102400-44122600	Weak transcription	NHDF-Ad	bronchial
6	chr19:44102600-44120600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:44102600-44121200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr19:44102600-44122600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr19:44102600-44122600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr19:44102800-44120000	Strong transcription	Fetal Stomach	stomach
11	chr19:44104400-44122800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr19:44104800-44123000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:44106000-44120000	Weak transcription	Right Atrium	heart
14	chr19:44106000-44122600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr19:44106200-44122800	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr19:44109400-44118800	Strong transcription	Dnd41	blood
17	chr19:44110600-44119800	Strong transcription	Fetal Muscle Trunk	muscle
18	chr19:44111600-44120400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:44112000-44118600	Strong transcription	Thymus	Thymus
20	chr19:44112000-44119200	Strong transcription	Fetal Muscle Leg	muscle
21	chr19:44112000-44122600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr19:44112200-44120800	Weak transcription	Fetal Brain Male	brain
23	chr19:44112400-44118600	Strong transcription	Fetal Brain Female	brain
24	chr19:44112600-44122600	Weak transcription	HUVEC	blood vessel
25	chr19:44113800-44118800	Strong transcription	Spleen	Spleen
26	chr19:44113800-44119200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr19:44113800-44119200	Strong transcription	Fetal Intestine Small	intestine
28	chr19:44113800-44119400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:44114000-44118600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr19:44114000-44119200	Strong transcription	Primary T cells from cord blood	blood
31	chr19:44114200-44118400	Strong transcription	Lung	lung
32	chr19:44114800-44118400	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr19:44114800-44118400	Strong transcription	Liver	Liver
34	chr19:44114800-44118600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr19:44114800-44118600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr19:44114800-44118600	Strong transcription	A549	lung
37	chr19:44114800-44119200	Strong transcription	Fetal Thymus	thymus
38	chr19:44114800-44119400	Strong transcription	Colon Smooth Muscle	Colon
39	chr19:44115000-44118600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr19:44115000-44118600	Strong transcription	Brain Hippocampus Middle	brain
41	chr19:44115000-44118600	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr19:44115000-44118600	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr19:44115200-44118400	Strong transcription	Adipose Nuclei	Adipose
44	chr19:44115200-44118800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:44115200-44119200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:44115400-44118600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr19:44115400-44118800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr19:44115400-44119800	Weak transcription	K562	blood
49	chr19:44115600-44118600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr19:44115600-44119400	Strong transcription	Cortex derived primary cultured neurospheres	brain

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