Variant report

Variant	rs880108
Chromosome Location	chr19:44115140-44115141
allele	G/T
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	POLR2A	chr19:44115103-44115319	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44098915..44102164-chr19:44112167..44115504,5	K562	blood:
2	chr19:44099192..44100821-chr19:44114703..44116674,2	MCF-7	breast:

Variant related genes	Relation type
SRRM5	TF binding region
ENSG00000124444	Chromatin interaction
ENSG00000167378	Chromatin interaction
ENSG00000226763	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11083711	1.00[LWK][hapmap]
rs11083712	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11671645	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12461175	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1402325	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1402326	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17655574	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1879387	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2003098	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2079646	1.00[CEU][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2302421	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]
rs3746002	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3746003	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3815422	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803643	0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4803644	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73038867	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs767540	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs880108	ZNF615	cis	cerebellum	SCAN
rs880108	AKT1S1	cis	parietal	SCAN
rs880108	IZUMO2	cis	parietal	SCAN
rs880108	PRRG2	cis	cerebellum	SCAN
rs880108	ZNF480	cis	parietal	SCAN
rs880108	PLAUR	cis	multi-tissue	Pritchard

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	chr19:44102600-44115800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr19:44102600-44116200	Weak transcription	Hela-S3	cervix
8	chr19:44102600-44120600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:44102600-44121200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr19:44102600-44122600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr19:44102600-44122600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr19:44102800-44120000	Strong transcription	Fetal Stomach	stomach
13	chr19:44104000-44116000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr19:44104000-44116200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr19:44104400-44122800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr19:44104600-44115800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr19:44104600-44116200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr19:44104600-44116400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr19:44104800-44123000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr19:44105200-44115800	Weak transcription	HSMM	muscle
21	chr19:44105800-44116200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr19:44106000-44120000	Weak transcription	Right Atrium	heart
23	chr19:44106000-44122600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr19:44106200-44116000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr19:44106200-44122800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr19:44106400-44116000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr19:44106800-44115800	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr19:44107000-44115800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr19:44107200-44116400	Weak transcription	Ovary	ovary
30	chr19:44107200-44116600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr19:44107400-44115800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr19:44107400-44116200	Weak transcription	Fetal Intestine Large	intestine
33	chr19:44109400-44118800	Strong transcription	Dnd41	blood
34	chr19:44110600-44119800	Strong transcription	Fetal Muscle Trunk	muscle
35	chr19:44111200-44116000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr19:44111400-44116000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr19:44111400-44116000	Weak transcription	Brain Angular Gyrus	brain
38	chr19:44111600-44115800	Weak transcription	HepG2	liver
39	chr19:44111600-44116200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr19:44111600-44120400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr19:44111800-44115800	Weak transcription	GM12878-XiMat	blood
42	chr19:44111800-44116000	Weak transcription	NHEK	skin
43	chr19:44112000-44118600	Strong transcription	Thymus	Thymus
44	chr19:44112000-44119200	Strong transcription	Fetal Muscle Leg	muscle
45	chr19:44112000-44122600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr19:44112200-44115800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr19:44112200-44115800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr19:44112200-44116000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr19:44112200-44116000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr19:44112200-44116000	Weak transcription	Primary B cells from cord blood	blood

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