Variant report

Variant	rs28399454
Chromosome Location	chr19:41351267-41351268
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:4474827..4477394-chr19:41351022..41353007,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103423	Chromatin interaction
ENSG00000262246	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10405934	1.00[CEU][hapmap]
rs10418304	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10422346	1.00[EUR][1000 genomes]
rs12721652	1.00[CEU][hapmap]
rs16974794	1.00[EUR][1000 genomes]
rs16974893	1.00[CEU][hapmap]
rs1962261	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs28399441	1.00[EUR][1000 genomes]
rs28739581	1.00[EUR][1000 genomes]
rs35950631	1.00[EUR][1000 genomes]
rs55768417	1.00[EUR][1000 genomes]
rs56164728	1.00[EUR][1000 genomes]
rs56194122	1.00[EUR][1000 genomes]
rs57484466	1.00[EUR][1000 genomes]
rs60618718	1.00[EUR][1000 genomes]
rs60923425	1.00[EUR][1000 genomes]
rs61402679	1.00[EUR][1000 genomes]
rs61466079	1.00[EUR][1000 genomes]
rs61557439	1.00[EUR][1000 genomes]
rs714097	1.00[EUR][1000 genomes]
rs7247532	1.00[EUR][1000 genomes]
rs7250597	1.00[CEU][hapmap]
rs7259758	1.00[EUR][1000 genomes]
rs73557121	1.00[EUR][1000 genomes]
rs73557149	1.00[EUR][1000 genomes]
rs73557170	1.00[EUR][1000 genomes]
rs73559241	1.00[EUR][1000 genomes]
rs73933721	1.00[EUR][1000 genomes]
rs8100958	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs8105382	1.00[EUR][1000 genomes]
rs8105465	1.00[EUR][1000 genomes]
rs8106305	1.00[EUR][1000 genomes]
rs8107218	1.00[EUR][1000 genomes]
rs8107990	1.00[EUR][1000 genomes]
rs8109477	1.00[EUR][1000 genomes]
rs8112043	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs8112781	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs8192722	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:90 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758500	chr19:41291627-41546068	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2758762	chr19:41291627-41546068	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1066637	chr19:41309211-41597896	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv911729	chr19:41321372-41383828	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv2760509	chr19:41325004-41394336	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1056244	chr19:41329218-41397661	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv1827726	chr19:41329872-41395056	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv1832156	chr19:41332004-41399077	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv817836	chr19:41333284-41363765	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1058732	chr19:41334726-41368987	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv1058747	chr19:41334726-41376007	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	esv2763010	chr19:41334738-41380946	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	esv14395	chr19:41337301-41393256	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv9729	chr19:41337805-41394407	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv911730	chr19:41337923-41356054	Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv911731	chr19:41337923-41356751	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	nsv911732	chr19:41337923-41372475	Strong transcription Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv911733	chr19:41337923-41383828	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
19	nsv911734	chr19:41337923-41392885	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
20	esv1830996	chr19:41338610-41391238	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
21	esv1832383	chr19:41338610-41393111	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
22	nsv1057349	chr19:41338835-41368987	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
23	nsv1062369	chr19:41338835-41369393	Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
24	nsv1055204	chr19:41338835-41369697	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
25	nsv1063224	chr19:41338835-41370781	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
26	nsv1055758	chr19:41338835-41370835	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
27	nsv1063909	chr19:41338835-41370933	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
28	nsv1066061	chr19:41338835-41376007	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
29	nsv1057452	chr19:41338835-41380934	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
30	nsv1057412	chr19:41339857-41368987	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
31	nsv1066701	chr19:41339857-41369697	Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
32	nsv1066884	chr19:41339857-41370835	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
33	nsv1064519	chr19:41339857-41375954	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
34	nsv1059038	chr19:41339857-41380934	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
35	nsv1065886	chr19:41339857-41397661	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
36	esv33053	chr19:41340629-41400635	Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
37	nsv911735	chr19:41341589-41356054	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
38	nsv911736	chr19:41341589-41356751	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
39	nsv516972	chr19:41341589-41363765	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
40	nsv579525	chr19:41341589-41372475	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
41	nsv911737	chr19:41341589-41372475	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
42	nsv911738	chr19:41341589-41379148	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
43	nsv911740	chr19:41341589-41383799	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
44	nsv911739	chr19:41341589-41383828	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
45	esv3335352	chr19:41345075-41375737	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
46	nsv1062605	chr19:41345146-41368987	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
47	nsv1062739	chr19:41345146-41369697	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
48	nsv1058924	chr19:41345146-41370933	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
49	nsv1067231	chr19:41345146-41380934	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
50	esv3584737	chr19:41345158-41380946	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41349800-41353800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:41350000-41351400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr19:41350000-41352600	Weak transcription	Lung	lung
4	chr19:41350000-41353000	Strong transcription	Liver	Liver
5	chr19:41350600-41354400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr19:41350800-41354400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr19:41351000-41354600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr19:41351200-41354400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr19:41351200-41354400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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