Variant report

Variant	rs3745528
Chromosome Location	chr19:51302066-51302067
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:0)
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	chr19:51301541..51303220-chr19:51379402..51381773,3	K562	blood:
2	chr19:51301551..51303392-chr19:51334103..51335973,2	K562	blood:
3	chr19:51297152..51303261-chr19:51371696..51377038,8	K562	blood:
4	chr19:51226381..51234126-chr19:51290973..51302468,19	K562	blood:
5	chr19:51301276..51304039-chr19:51527305..51529932,2	MCF-7	breast:
6	chr19:51192657..51194532-chr19:51298388..51302132,3	K562	blood:
7	chr19:51300732..51302357-chr19:51358771..51360545,2	K562	blood:
8	chr19:51291326..51293896-chr19:51301181..51304163,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000167757	Chromatin interaction
ENSG00000174562	Chromatin interaction
ENSG00000142513	Chromatin interaction
ENSG00000161681	Chromatin interaction
ENSG00000105472	Chromatin interaction
ENSG00000167751	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10401588	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1043315	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10853825	0.83[CHD][hapmap];0.82[LWK][hapmap];0.91[YRI][hapmap]
rs11668685	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11668998	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12052047	0.81[ASW][hapmap];0.83[CHD][hapmap]
rs12610777	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288417	0.81[ASW][hapmap];0.83[CHD][hapmap];0.82[YRI][hapmap]
rs3212846	0.81[ASW][hapmap];0.83[CHD][hapmap]
rs3745526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3865442	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3909863	0.83[CHD][hapmap]
rs4801853	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802741	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802742	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs5517	0.81[CHD][hapmap]
rs5519	0.83[CHD][hapmap]
rs55735528	0.86[AMR][1000 genomes]
rs55929248	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258708	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9991	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060760	chr19:50883425-51463712	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1058177	chr19:50984774-51463712	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv912288	chr19:51283791-51334355	Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
4	nsv912289	chr19:51283791-51335943	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
5	nsv912290	chr19:51283791-51344483	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
6	nsv526232	chr19:51301230-51335943	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3745528	C19orf48	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51291800-51303400	Weak transcription	Fetal Kidney	kidney
2	chr19:51296600-51304200	Weak transcription	HSMM	muscle
3	chr19:51297000-51306200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr19:51297600-51304200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr19:51297800-51305600	Weak transcription	Fetal Brain Male	brain
6	chr19:51297800-51306200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr19:51298000-51303000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr19:51298000-51305400	Weak transcription	Fetal Heart	heart
9	chr19:51298200-51305400	Strong transcription	Fetal Intestine Small	intestine
10	chr19:51298200-51305400	Strong transcription	Fetal Stomach	stomach
11	chr19:51298200-51305800	Strong transcription	Brain Germinal Matrix	brain
12	chr19:51298200-51306000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr19:51298200-51306800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr19:51298400-51304400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:51298400-51304600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr19:51298400-51305400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:51298400-51305400	Strong transcription	Fetal Muscle Leg	muscle
18	chr19:51298400-51305800	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr19:51298600-51303400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr19:51298600-51304600	Strong transcription	Duodenum Mucosa	Duodenum
21	chr19:51298600-51305000	Strong transcription	Thymus	Thymus
22	chr19:51298600-51305200	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr19:51298600-51305400	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr19:51298600-51305400	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr19:51298600-51305400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr19:51298600-51305400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr19:51298600-51305600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:51298600-51305600	Strong transcription	Fetal Brain Female	brain
29	chr19:51298800-51302200	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr19:51298800-51302400	Strong transcription	Primary T cells from cord blood	blood
31	chr19:51298800-51303400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr19:51298800-51304600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr19:51298800-51305200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr19:51298800-51305400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr19:51298800-51305400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr19:51298800-51305400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr19:51298800-51305600	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr19:51299000-51303000	Strong transcription	Dnd41	blood
39	chr19:51299000-51304200	Strong transcription	HMEC	breast
40	chr19:51299000-51305400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr19:51299000-51305400	Strong transcription	Liver	Liver
42	chr19:51299200-51302800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:51299200-51304000	Strong transcription	Esophagus	oesophagus
44	chr19:51299200-51305800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr19:51299400-51305000	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr19:51299400-51305400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr19:51299400-51305600	Weak transcription	NHDF-Ad	bronchial
48	chr19:51299400-51305800	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr19:51299600-51304000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr19:51299600-51304600	Strong transcription	Primary T helper cells fromperipheralblood	blood

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