Variant report

Variant	rs28668750
Chromosome Location	chr19:39819802-39819803
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39808144..39812302-chr19:39816588..39820391,4	MCF-7	breast:
2	chr19:39799131..39802909-chr19:39818026..39820396,4	K562	blood:
3	chr19:39817477..39820007-chr19:39829968..39833283,3	MCF-7	breast:
4	chr19:39818815..39820498-chr19:39824336..39826282,2	K562	blood:
5	chr19:39798143..39803164-chr19:39817466..39820362,4	K562	blood:
6	chr19:39683585..39686543-chr19:39818875..39821716,2	MCF-7	breast:
7	chr19:39615312..39617017-chr19:39817351..39819854,2	MCF-7	breast:
8	chr19:39818884..39821188-chr19:39900599..39903098,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000130755	Chromatin interaction
ENSG00000269246	Chromatin interaction
ENSG00000268262	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000130669	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs16973374	0.81[JPT][hapmap]
rs194016	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs251903	0.83[CEU][hapmap]
rs251906	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs251907	0.85[ASN][1000 genomes]
rs30453	0.89[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs30454	0.89[CHB][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs30455	0.89[CHB][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs30457	0.89[CHB][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs30480	0.82[CEU][hapmap]
rs34605107	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34615060	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36264	0.89[CHB][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs36270	0.83[GIH][hapmap]
rs39587	0.91[CEU][hapmap]
rs40441	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs562638	0.89[CHB][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs6508860	0.82[JPT][hapmap]
rs685125	0.89[CHB][hapmap];0.81[GIH][hapmap]
rs8108034	0.91[CEU][hapmap]
rs917319	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv833830	chr19:39709538-39837846	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
4	nsv1058514	chr19:39744112-39902580	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
6	nsv911681	chr19:39797716-39856246	Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
7	esv10629	chr19:39811570-39886212	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39811400-39825800	Weak transcription	Gastric	stomach
2	chr19:39812000-39825600	Weak transcription	Right Ventricle	heart
3	chr19:39814800-39826000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr19:39816400-39820000	Strong transcription	Thymus	Thymus
5	chr19:39816800-39821400	Weak transcription	Fetal Intestine Small	intestine
6	chr19:39817000-39822000	Strong transcription	Primary hematopoietic stem cells	blood
7	chr19:39817000-39822200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr19:39817000-39822600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
9	chr19:39817000-39823200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
10	chr19:39817000-39824000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
11	chr19:39817000-39824600	Genic enhancers	Primary T cells fromperipheralblood	blood
12	chr19:39817200-39825800	Weak transcription	Placenta	Placenta
13	chr19:39817400-39821600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr19:39817600-39820400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr19:39817600-39821200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr19:39817600-39822400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr19:39817600-39823600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:39817800-39822200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr19:39817800-39822800	Strong transcription	Spleen	Spleen
20	chr19:39817800-39823000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr19:39817800-39824400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr19:39818000-39822400	Strong transcription	Lung	lung
23	chr19:39818200-39820400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr19:39818400-39820000	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:39818400-39820000	Genic enhancers	Fetal Thymus	thymus
26	chr19:39818400-39820200	Genic enhancers	Monocytes-CD14+_RO01746	blood
27	chr19:39818400-39820400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr19:39818400-39822000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr19:39818600-39820200	Genic enhancers	Dnd41	blood
30	chr19:39818600-39820400	Genic enhancers	Primary B cells from peripheral blood	blood
31	chr19:39818600-39822600	Genic enhancers	Primary T cells from cord blood	blood
32	chr19:39818600-39831600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr19:39818800-39821200	Weak transcription	Fetal Intestine Large	intestine
34	chr19:39818800-39825800	Weak transcription	Left Ventricle	heart
35	chr19:39818800-39826800	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr19:39819000-39820000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr19:39819000-39820800	Enhancers	Liver	Liver
38	chr19:39819200-39820000	Weak transcription	Adipose Nuclei	Adipose
39	chr19:39819200-39821600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr19:39819200-39821600	Weak transcription	A549	lung
41	chr19:39819200-39825000	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr19:39819200-39825200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr19:39819200-39825800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr19:39819200-39825800	Weak transcription	K562	blood
45	chr19:39819400-39820000	Weak transcription	Pancreas	Pancrea
46	chr19:39819600-39820000	Genic enhancers	GM12878-XiMat	blood
47	chr19:39819600-39820200	Enhancers	Duodenum Mucosa	Duodenum
48	chr19:39819800-39820400	Strong transcription	Primary B cells from cord blood	blood

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