Variant report

Variant	rs814519
Chromosome Location	chr19:41084863-41084864
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	SIX5	chr19:41084368-41084871	GM12878	blood:	n/a	chr19:41084494-41084503 chr19:41084555-41084564 chr19:41084492-41084506 chr19:41084681-41084690 chr19:41084496-41084505 chr19:41084557-41084566 chr19:41084679-41084688
2	IRF1	chr19:41084378-41085025	K562	blood:	n/a	n/a
3	ELF1	chr19:41084281-41084868	K562	blood:	n/a	n/a
4	ETS1	chr19:41084310-41084876	A549	lung:	n/a	chr19:41084680-41084687 chr19:41084678-41084691 chr19:41084679-41084692 chr19:41084492-41084505 chr19:41084555-41084568 chr19:41084554-41084567
5	NFYB	chr19:41084806-41084945	GM12878	blood:	n/a	chr19:41084848-41084861
6	ETS1	chr19:41084346-41084874	K562	blood:	n/a	chr19:41084680-41084687 chr19:41084678-41084691 chr19:41084679-41084692 chr19:41084492-41084505 chr19:41084555-41084568 chr19:41084554-41084567
7	SIX5	chr19:41084208-41084868	H1-hESC	embryonic stem cell:	n/a	chr19:41084494-41084503 chr19:41084555-41084564 chr19:41084492-41084506 chr19:41084681-41084690 chr19:41084496-41084505 chr19:41084557-41084566 chr19:41084679-41084688
8	SIX5	chr19:41084254-41084964	A549	lung:	n/a	chr19:41084494-41084503 chr19:41084555-41084564 chr19:41084492-41084506 chr19:41084681-41084690 chr19:41084496-41084505 chr19:41084557-41084566 chr19:41084679-41084688
9	ZNF143	chr19:41084282-41084916	GM12878	blood:	n/a	chr19:41084494-41084503 chr19:41084496-41084505 chr19:41084555-41084564 chr19:41084672-41084690 chr19:41084557-41084566 chr19:41084681-41084690 chr19:41084494-41084512 chr19:41084679-41084688
10	ZNF143	chr19:41084115-41084990	K562	blood:	n/a	chr19:41084494-41084503 chr19:41084496-41084505 chr19:41084555-41084564 chr19:41084672-41084690 chr19:41084557-41084566 chr19:41084681-41084690 chr19:41084494-41084512 chr19:41084679-41084688
11	NFYB	chr19:41084419-41084863	K562	blood:	n/a	chr19:41084848-41084861
12	TBL1XR1	chr19:41084437-41084911	K562	blood:	n/a	n/a
13	ZNF143	chr19:41084105-41084949	H1-hESC	embryonic stem cell:	n/a	chr19:41084494-41084503 chr19:41084496-41084505 chr19:41084555-41084564 chr19:41084672-41084690 chr19:41084557-41084566 chr19:41084681-41084690 chr19:41084494-41084512 chr19:41084679-41084688
14	SIX5	chr19:41084273-41084883	K562	blood:	n/a	chr19:41084494-41084503 chr19:41084555-41084564 chr19:41084492-41084506 chr19:41084681-41084690 chr19:41084496-41084505 chr19:41084557-41084566 chr19:41084679-41084688
15	SIX5	chr19:41084055-41084999	A549	lung:	n/a	chr19:41084494-41084503 chr19:41084555-41084564 chr19:41084492-41084506 chr19:41084681-41084690 chr19:41084496-41084505 chr19:41084557-41084566 chr19:41084679-41084688
16	SIX5	chr19:41084274-41084947	H1-hESC	embryonic stem cell:	n/a	chr19:41084494-41084503 chr19:41084555-41084564 chr19:41084492-41084506 chr19:41084681-41084690 chr19:41084496-41084505 chr19:41084557-41084566 chr19:41084679-41084688
17	SIX5	chr19:41084270-41084863	K562	blood:	n/a	chr19:41084494-41084503 chr19:41084555-41084564 chr19:41084492-41084506 chr19:41084681-41084690 chr19:41084496-41084505 chr19:41084557-41084566 chr19:41084679-41084688
18	GABPA	chr19:41084324-41084991	A549	lung:	n/a	n/a
19	ELF1	chr19:41084175-41084876	HCT-116	colon:	n/a	n/a
20	HCFC1	chr19:41084158-41084925	K562	blood:	n/a	n/a
21	ZNF143	chr19:41084297-41084907	Hela-S3	cervix:	n/a	chr19:41084494-41084503 chr19:41084496-41084505 chr19:41084555-41084564 chr19:41084672-41084690 chr19:41084557-41084566 chr19:41084681-41084690 chr19:41084494-41084512 chr19:41084679-41084688
22	HCFC1	chr19:41084170-41084887	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41082477..41084504-chr19:41084701..41086992,2	K562	blood:
2	chr19:41073482..41079307-chr19:41080637..41087483,13	K562	blood:
3	chr19:40949356..40951843-chr19:41083113..41086048,2	MCF-7	breast:
4	chr19:41083433..41086530-chr19:41091695..41093965,3	MCF-7	breast:
5	chr19:41084074..41087113-chr19:41095673..41098662,4	K562	blood:
6	chr19:41083100..41084650-chr19:41084700..41086878,2	MCF-7	breast:
7	chr19:41083044..41086167-chr19:41095673..41098202,4	K562	blood:
8	chr19:41084714..41088277-chr19:41106890..41109795,3	K562	blood:
9	chr19:40853029..40856025-chr19:41082472..41085390,2	K562	blood:
10	chr19:41074012..41077627-chr19:41080511..41085417,7	MCF-7	breast:

Variant related genes	Relation type
SHKBP1	TF binding region
ENSG00000160460	Chromatin interaction
ENSG00000167565	Chromatin interaction
ENSG00000160410	Chromatin interaction
ENSG00000105223	Chromatin interaction
ENSG00000160392	Chromatin interaction
ENSG00000090006	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs16974365	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[ASN][1000 genomes]
rs2290682	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs418007	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs421739	0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803346	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58633563	0.92[ASN][1000 genomes]
rs62107871	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62107874	0.83[ASN][1000 genomes]
rs710160	0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs814518	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv911714	chr19:41006426-41165252	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer 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	33 gene(s)	inside rSNPs	diseases
3	nsv911715	chr19:41014922-41141434	Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv1057634	chr19:41019512-41174259	Enhancers Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv911716	chr19:41023511-41109456	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv911717	chr19:41023511-41141434	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv911719	chr19:41033109-41147087	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv911720	chr19:41033109-41156940	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv911721	chr19:41040334-41124931	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong 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	33 gene(s)	inside rSNPs	diseases
10	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
12	nsv869561	chr19:41077513-41139834	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs814519	B9D2	cis	parietal	SCAN
rs814519	PGLYRP1	cis	cerebellum	SCAN
rs814519	LTBP4	cis	multi-tissue	Pritchard
rs814519	GRWD1	cis	parietal	SCAN
rs814519	DMRTC2	cis	cerebellum	SCAN
rs814519	CA11	cis	cerebellum	SCAN
rs814519	QPCTL	cis	cerebellum	SCAN
rs814519	KCNN4	cis	cerebellum	SCAN
rs814519	NDUFAF2	trans	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41083600-41085000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
2	chr19:41083600-41085400	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
3	chr19:41083600-41085600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr19:41083600-41086000	Weak transcription	Fetal Brain Female	brain
5	chr19:41083600-41086000	Weak transcription	NH-A	brain
6	chr19:41083600-41086200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr19:41083600-41086200	Enhancers	Primary hematopoietic stem cells	blood
8	chr19:41083600-41086200	Weak transcription	Aorta	Aorta
9	chr19:41083600-41086200	Weak transcription	Ovary	ovary
10	chr19:41083600-41086200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr19:41083600-41086400	Weak transcription	Brain Anterior Caudate	brain
12	chr19:41083600-41086600	Genic enhancers	Primary B cells from peripheral blood	blood
13	chr19:41083600-41091200	Weak transcription	Psoas Muscle	Psoas
14	chr19:41083600-41092800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:41083600-41093600	Weak transcription	Fetal Lung	lung
16	chr19:41083600-41095400	Weak transcription	Fetal Kidney	kidney
17	chr19:41083600-41100400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr19:41083600-41101000	Weak transcription	HSMMtube	muscle
19	chr19:41083800-41085400	Genic enhancers	Primary T cells fromperipheralblood	blood
20	chr19:41083800-41086000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr19:41083800-41086000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr19:41083800-41086000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:41083800-41086000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr19:41083800-41086000	Weak transcription	Fetal Intestine Large	intestine
25	chr19:41083800-41086000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr19:41083800-41086000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr19:41083800-41086200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr19:41083800-41086200	Weak transcription	Brain Germinal Matrix	brain
29	chr19:41083800-41086800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:41083800-41086800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr19:41084000-41086000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr19:41084000-41086200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr19:41084000-41086200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr19:41084000-41087800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr19:41084000-41089800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:41084000-41091600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr19:41084000-41094000	Weak transcription	HSMM	muscle
38	chr19:41084000-41095400	Strong transcription	Fetal Intestine Small	intestine
39	chr19:41084000-41097600	Strong transcription	Fetal Stomach	stomach
40	chr19:41084200-41085000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:41084200-41085000	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr19:41084200-41085000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr19:41084200-41085000	Strong transcription	NHLF	lung
44	chr19:41084200-41085200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr19:41084200-41085200	Genic enhancers	Primary B cells from cord blood	blood
46	chr19:41084200-41085200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr19:41084200-41085400	Enhancers	GM12878-XiMat	blood
48	chr19:41084200-41085400	Weak transcription	Osteobl	bone
49	chr19:41084200-41085600	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr19:41084200-41086000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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