Variant report

Variant	rs107878
Chromosome Location	chr19:36250259-36250260
allele	C/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	MAX	chr19:36249987-36250427	K562	blood:	n/a	chr19:36250240-36250247 chr19:36250237-36250250 chr19:36250238-36250248 chr19:36250239-36250249 chr19:36250238-36250249 chr19:36250239-36250248 chr19:36250238-36250247 chr19:36250237-36250252 chr19:36250235-36250250 chr19:36250237-36250250 chr19:36250239-36250248

No.	Distal block	Cell Line	Cell type
1	chr19:36249097..36250751-chr19:36253279..36257027,3	K562	blood:
2	chr19:36247404..36252021-chr19:36265348..36272678,7	MCF-7	breast:
3	chr19:36248580..36254743-chr19:36274692..36280659,6	K562	blood:
4	chr19:36206099..36210841-chr19:36246614..36251827,8	MCF-7	breast:
5	chr19:36249138..36251092-chr19:36255483..36258452,2	MCF-7	breast:
6	chr19:36248761..36250845-chr19:36272724..36275459,2	MCF-7	breast:
7	chr19:36231491..36233720-chr19:36248400..36250494,2	MCF-7	breast:
8	chr19:36238866..36244880-chr19:36246037..36252437,21	MCF-7	breast:
9	chr19:36247584..36253409-chr19:36264102..36268750,7	K562	blood:

Variant related genes	Relation type
C19orf55	TF binding region
HSPB6	TF binding region
ENSG00000267439	Chromatin interaction
ENSG00000272333	Chromatin interaction
ENSG00000004777	Chromatin interaction
ENSG00000126246	Chromatin interaction
ENSG00000167595	Chromatin interaction
ENSG00000267796	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11084828	0.86[CEU][hapmap];0.89[GIH][hapmap];0.89[LWK][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs11667696	0.92[CEU][hapmap];0.94[GIH][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11670414	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11671520	0.80[EUR][1000 genomes]
rs11672164	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12151356	0.80[EUR][1000 genomes]
rs12609803	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17776911	0.93[CEU][hapmap];0.86[GIH][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2293687	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3746278	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3787051	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3848663	0.93[CEU][hapmap];0.86[GIH][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3885794	0.81[EUR][1000 genomes]
rs3885795	0.81[EUR][1000 genomes]
rs4806197	0.93[CEU][hapmap];0.84[GIH][hapmap];0.85[LWK][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs4806198	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4806201	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806202	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58561864	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs66747537	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
3	nsv458566	chr19:36156588-36265508	Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv579422	chr19:36156588-36265508	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv911631	chr19:36169285-36290977	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv911632	chr19:36174176-36288297	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv911633	chr19:36206050-36283847	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
8	nsv911634	chr19:36206050-36290977	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
9	nsv543996	chr19:36210269-36265431	Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv1057830	chr19:36210269-36279794	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer 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	43 gene(s)	inside rSNPs	diseases
11	nsv543997	chr19:36210269-36279794	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
12	nsv911635	chr19:36217333-36283847	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv458567	chr19:36221051-36283847	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
14	nsv579423	chr19:36221051-36283847	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
15	nsv911636	chr19:36240960-36290977	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs107878	FBXO17	cis	cerebellum	SCAN
rs107878	DEDD2	cis	cerebellum	SCAN
rs107878	LYPD3	cis	parietal	SCAN
rs107878	U2AF1L3	cis	multi-tissue	Pritchard
rs107878	ZNF780B	cis	cerebellum	SCAN
rs107878	NFKBIB	cis	cerebellum	SCAN
rs107878	CEACAM4	cis	cerebellum	SCAN
rs107878	ZFP36	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36248400-36250600	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr19:36248400-36250800	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr19:36249400-36251400	Enhancers	Spleen	Spleen
4	chr19:36249600-36250400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr19:36249600-36250400	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr19:36249600-36250400	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr19:36249600-36250400	Flanking Active TSS	Brain Anterior Caudate	brain
8	chr19:36249600-36250400	Flanking Active TSS	Brain Germinal Matrix	brain
9	chr19:36249600-36250400	Enhancers	Fetal Brain Male	brain
10	chr19:36249600-36250400	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr19:36249600-36250400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr19:36249600-36250600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr19:36249600-36250800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr19:36249600-36250800	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr19:36249600-36251000	Enhancers	Primary B cells from peripheral blood	blood
16	chr19:36249600-36251000	Enhancers	Fetal Heart	heart
17	chr19:36249600-36251000	Enhancers	Pancreas	Pancrea
18	chr19:36249600-36251400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr19:36249600-36251800	Weak transcription	Ovary	ovary
20	chr19:36249600-36252600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:36249800-36250400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr19:36249800-36250400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:36249800-36250400	Enhancers	Colonic Mucosa	Colon
24	chr19:36249800-36250400	Enhancers	Rectal Smooth Muscle	rectum
25	chr19:36249800-36250400	Enhancers	Thymus	Thymus
26	chr19:36249800-36250400	Flanking Active TSS	GM12878-XiMat	blood
27	chr19:36249800-36250400	Flanking Active TSS	HMEC	breast
28	chr19:36249800-36250600	Enhancers	Primary T cells fromperipheralblood	blood
29	chr19:36249800-36250600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:36249800-36250600	Enhancers	Placenta	Placenta
31	chr19:36249800-36250600	Enhancers	Stomach Mucosa	stomach
32	chr19:36249800-36250800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:36249800-36250800	Enhancers	Primary T cells from cord blood	blood
34	chr19:36249800-36250800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr19:36249800-36250800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr19:36249800-36250800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr19:36249800-36250800	Enhancers	Brain Angular Gyrus	brain
38	chr19:36249800-36250800	Enhancers	Lung	lung
39	chr19:36249800-36250800	Enhancers	Placenta Amnion	Placenta Amnion
40	chr19:36249800-36251000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr19:36249800-36251000	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr19:36249800-36251000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr19:36249800-36251800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:36249800-36251800	Weak transcription	HSMMtube	muscle
45	chr19:36249800-36255000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr19:36249800-36265600	Weak transcription	Right Atrium	heart
47	chr19:36249800-36265800	Weak transcription	Fetal Kidney	kidney
48	chr19:36250000-36250400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr19:36250000-36250400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr19:36250000-36250400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links