Variant report

Variant	rs274154
Chromosome Location	chr19:56671836-56671837
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:56651508..56653852-chr19:56670143..56672532,2	K562	blood:
2	chr19:56671026..56674616-chr19:56677144..56679269,3	K562	blood:
3	chr19:56670800..56672784-chr19:56675448..56678240,2	MCF-7	breast:
4	chr19:56629489..56634220-chr19:56669438..56672603,6	K562	blood:
5	chr19:56664832..56668754-chr19:56669452..56673649,4	K562	blood:

Variant related genes	Relation type
ENSG00000167685	Chromatin interaction
ENSG00000142409	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs2631642	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2631652	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs274141	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs274144	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs274145	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs274146	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs274151	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs274155	0.86[CHB][hapmap]
rs274156	0.89[CEU][hapmap];0.84[CHB][hapmap];0.84[EUR][1000 genomes]
rs274159	0.90[CEU][hapmap];0.85[CHB][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs274163	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs274165	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs274167	0.83[EUR][1000 genomes]
rs274168	0.85[MEX][hapmap]
rs274180	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs274182	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3103059	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3103060	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs480528	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs481291	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs482506	0.86[ASN][1000 genomes]
rs487922	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs488118	0.86[ASN][1000 genomes]
rs488196	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs565171	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs581486	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61283021	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs650832	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs651800	0.86[ASN][1000 genomes]
rs652204	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs671061	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs672956	0.81[ASN][1000 genomes]
rs679082	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs901476	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056598	chr19:56331762-56703428	Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	nsv1064371	chr19:56418215-56842450	ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
3	nsv1057316	chr19:56418215-56849458	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv580354	chr19:56505685-56723492	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
5	nsv523651	chr19:56537528-56707048	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	nsv1057820	chr19:56555942-56720262	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
7	nsv528998	chr19:56578238-56707048	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv517365	chr19:56592286-56674548	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	nsv912513	chr19:56592286-56685463	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
10	nsv521744	chr19:56592286-56686953	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
11	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
12	nsv528361	chr19:56638845-56688570	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	esv3427270	chr19:56670165-56672713	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56653800-56673000	Weak transcription	Hela-S3	cervix
2	chr19:56653800-56674000	Weak transcription	Fetal Kidney	kidney
3	chr19:56654000-56681600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr19:56654200-56674000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr19:56655200-56672200	Weak transcription	NHDF-Ad	bronchial
6	chr19:56656400-56672200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr19:56659200-56673000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr19:56661400-56676200	Weak transcription	Fetal Brain Male	brain
9	chr19:56662000-56672200	Weak transcription	Fetal Heart	heart
10	chr19:56663000-56673200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr19:56663200-56674000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr19:56663800-56672400	Strong transcription	Dnd41	blood
13	chr19:56663800-56673000	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr19:56663800-56673600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr19:56664000-56672800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr19:56664000-56673000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr19:56664600-56672800	Strong transcription	Fetal Intestine Large	intestine
18	chr19:56664800-56672800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:56664800-56673800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr19:56664800-56673800	Strong transcription	Fetal Intestine Small	intestine
21	chr19:56665000-56674000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr19:56665200-56672400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:56665200-56673400	Strong transcription	Gastric	stomach
24	chr19:56665200-56674000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:56665200-56674400	Strong transcription	Fetal Stomach	stomach
26	chr19:56665400-56672800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr19:56665400-56673200	Weak transcription	HUVEC	blood vessel
28	chr19:56665400-56674000	Strong transcription	Stomach Smooth Muscle	stomach
29	chr19:56665400-56674200	Strong transcription	Fetal Brain Female	brain
30	chr19:56665600-56672600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr19:56665600-56672800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:56665600-56673200	Strong transcription	Thymus	Thymus
33	chr19:56665600-56673400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr19:56665800-56673000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr19:56665800-56674200	Strong transcription	Brain Germinal Matrix	brain
36	chr19:56666000-56672000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr19:56666000-56672400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr19:56666000-56672600	Strong transcription	Primary B cells from peripheral blood	blood
39	chr19:56666000-56672600	Strong transcription	Fetal Thymus	thymus
40	chr19:56666000-56672800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:56666000-56673000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:56666000-56673200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr19:56666000-56673200	Strong transcription	Placenta	Placenta
44	chr19:56666400-56673400	Strong transcription	Primary T cells from cord blood	blood
45	chr19:56666800-56673200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr19:56667000-56672400	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr19:56667000-56673400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr19:56667000-56673400	Strong transcription	Liver	Liver
49	chr19:56667000-56674800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr19:56667600-56672200	Weak transcription	GM12878-XiMat	blood

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