Variant report

Variant	rs16975329
Chromosome Location	chr19:42036793-42036794
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	POLR2A	chr19:42035639-42038770	GM12892	blood:	n/a	n/a
2	YY1	chr19:42036509-42036887	GM12892	blood:	n/a	n/a
3	POLR2A	chr19:42035603-42038761	GM12892	blood:	n/a	n/a
4	RUNX3	chr19:42035919-42036871	GM12878	blood:	n/a	chr19:42036623-42036632 chr19:42036623-42036632
5	MTA3	chr19:42035816-42037056	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:42035835-42038400	GM12892	blood:	n/a	n/a
7	POLR2A	chr19:42036122-42037263	GM12891	blood:	n/a	n/a
8	YY1	chr19:42036454-42036855	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:42035831-42038634	GM18505	blood:	n/a	n/a
10	SETDB1	chr19:42034208-42038482	U2OS	brain:	n/a	n/a
11	POLR2A	chr19:42036598-42036868	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:42035873-42037114	GM12891	blood:	n/a	n/a
13	RUNX3	chr19:42035847-42038620	GM12878	blood:	n/a	chr19:42036623-42036632 chr19:42036623-42036632
14	POLR2A	chr19:42036582-42036989	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:42035800-42038175	GM12891	blood:	n/a	n/a
16	POLR2A	chr19:42035790-42037005	GM12892	blood:	n/a	n/a
17	POLR2A	chr19:42035515-42038686	GM12891	blood:	n/a	n/a
18	POLR2A	chr19:42035667-42038718	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:42036098-42038153	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr19:42036227-42036885	GM12891	blood:	n/a	n/a
21	STAT5A	chr19:42036173-42036856	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000270164	TF binding region
ENSG00000268355	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11881771	0.89[EUR][1000 genomes]
rs16975336	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16975348	1.00[CEU][hapmap]
rs62119363	0.89[EUR][1000 genomes]
rs62119364	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119366	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119367	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119368	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119370	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119371	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119372	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119373	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119374	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119409	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62119416	1.00[EUR][1000 genomes]
rs62119419	0.89[EUR][1000 genomes]
rs62119420	0.89[EUR][1000 genomes]
rs62119421	0.89[EUR][1000 genomes]
rs62119449	0.89[EUR][1000 genomes]
rs62119450	0.89[EUR][1000 genomes]
rs7246864	0.89[EUR][1000 genomes]
rs7255763	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7255775	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7260464	1.00[CEU][hapmap]
rs9749229	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv510767	chr19:41962486-42049165	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv911770	chr19:41962486-42066279	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv911771	chr19:41962486-42085873	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1055515	chr19:41968797-42057334	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv911772	chr19:41985624-42066279	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv911773	chr19:42001210-42085873	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv579602	chr19:42015468-42047924	Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv978751	chr19:42036596-42073874	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42029800-42037600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:42033600-42037600	ZNF genes & repeats	GM12878-XiMat	blood
3	chr19:42034000-42037400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr19:42034200-42036800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr19:42034200-42036800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:42035000-42038400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:42035200-42036800	ZNF genes & repeats	Primary B cells from cord blood	blood
8	chr19:42035200-42037600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
9	chr19:42035400-42037200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:42035600-42037400	Enhancers	Primary T cells fromperipheralblood	blood
11	chr19:42035600-42037400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr19:42035800-42036800	ZNF genes & repeats	Adipose Nuclei	Adipose
13	chr19:42036000-42037400	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr19:42036200-42036800	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr19:42036200-42037000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr19:42036200-42037000	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:42036200-42037200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
18	chr19:42036200-42038000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr19:42036200-42038200	Active TSS	HSMMtube	muscle
20	chr19:42036400-42037000	ZNF genes & repeats	Lung	lung
21	chr19:42036400-42037200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr19:42036400-42038400	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr19:42036600-42036800	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr19:42036600-42036800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr19:42036600-42036800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
26	chr19:42036600-42036800	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr19:42036600-42036800	Weak transcription	Spleen	Spleen
28	chr19:42036600-42036800	Enhancers	HUVEC	blood vessel
29	chr19:42036600-42037000	Bivalent Enhancer	Thymus	Thymus
30	chr19:42036600-42037200	Enhancers	Left Ventricle	heart
31	chr19:42036600-42037400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr19:42036600-42038000	Bivalent Enhancer	Fetal Thymus	thymus
33	chr19:42036600-42038800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr19:42036600-42038800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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