Variant report

Variant	rs2599472
Chromosome Location	chr19:43951421-43951422
allele	G/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:43937028..43937653-chr19:43950851..43951764,3	MCF-7	breast:
2	chr19:43936721..43937673-chr19:43951109..43951816,2	MCF-7	breast:
3	chr19:43949852..43952277-chr19:44156357..44158096,2	K562	blood:
4	chr19:43950972..43953195-chr19:43955258..43957293,2	MCF-7	breast:
5	chr19:43950949..43953195-chr19:44029676..44031859,2	MCF-7	breast:
6	chr19:43949660..43952729-chr19:43966089..43969502,3	K562	blood:
7	chr19:43950829..43952315-chr19:44023277..44024591,13	MCF-7	breast:
8	chr19:43950463..43951811-chr19:44023286..44024411,8	MCF-7	breast:
9	chr19:43951229..43953633-chr19:43981664..43984219,2	MCF-7	breast:
10	chr19:43950879..43951915-chr19:44023292..44024529,15	K562	blood:

No data

Variant related genes	Relation type
ENSG00000105755	Chromatin interaction
ENSG00000124466	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2247798	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2599471	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2599474	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2599475	0.89[ASN][1000 genomes]
rs2682596	0.82[AMR][1000 genomes]
rs2682597	0.81[CHB][hapmap]
rs2682598	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35895695	0.81[ASN][1000 genomes]
rs3859443	0.80[CHB][hapmap]
rs4464191	0.81[CHB][hapmap]
rs4803630	0.81[CHB][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv1058162	chr19:43846238-44055058	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1060280	chr19:43866823-43959685	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv520852	chr19:43885085-43960114	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv579850	chr19:43885085-43960114	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv1066231	chr19:43918840-43954915	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	nsv579851	chr19:43920612-43955114	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
17	nsv1061862	chr19:43925290-43954915	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
18	nsv1058848	chr19:43925290-43957387	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
19	nsv2501	chr19:43942581-43978424	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:43943200-43953800	Weak transcription	Right Atrium	heart
2	chr19:43943800-43954800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr19:43944000-43956600	Weak transcription	Spleen	Spleen
4	chr19:43944200-43954800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:43944200-43954800	Weak transcription	Fetal Thymus	thymus
6	chr19:43948800-43951800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr19:43949800-43954800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:43950200-43954600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr19:43950400-43952400	Weak transcription	K562	blood
10	chr19:43950600-43951800	Enhancers	NHEK	skin
11	chr19:43951000-43951600	Enhancers	H9 Cell Line	embryonic stem cell
12	chr19:43951000-43951600	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr19:43951000-43951600	Enhancers	Primary T cells fromperipheralblood	blood
14	chr19:43951000-43951600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr19:43951000-43951600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr19:43951000-43951600	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr19:43951000-43951600	Enhancers	HepG2	liver
18	chr19:43951000-43951800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr19:43951000-43951800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr19:43951000-43951800	Enhancers	Primary B cells from peripheral blood	blood
21	chr19:43951000-43951800	Enhancers	Primary T cells from cord blood	blood
22	chr19:43951000-43951800	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr19:43951000-43951800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr19:43951000-43951800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr19:43951000-43951800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr19:43951000-43952000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr19:43951000-43952000	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr19:43951000-43952000	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr19:43951000-43952000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:43951200-43951600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:43951200-43951600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr19:43951200-43951600	Enhancers	Brain Cingulate Gyrus	brain
33	chr19:43951200-43951600	Enhancers	Brain Substantia Nigra	brain
34	chr19:43951200-43951600	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr19:43951200-43951600	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr19:43951200-43951800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr19:43951200-43951800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr19:43951200-43964800	Weak transcription	Esophagus	oesophagus
39	chr19:43951400-43951600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:43951400-43951600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:43951400-43951600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr19:43951400-43951600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr19:43951400-43951600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr19:43951400-43951600	Enhancers	Brain Angular Gyrus	brain
45	chr19:43951400-43951600	Enhancers	Brain Anterior Caudate	brain
46	chr19:43951400-43951600	Enhancers	Brain Hippocampus Middle	brain
47	chr19:43951400-43951600	Enhancers	Duodenum Mucosa	Duodenum
48	chr19:43951400-43951600	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr19:43951400-43951600	Enhancers	Placenta	Placenta
50	chr19:43951400-43951600	Enhancers	Osteobl	bone

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