Variant report

Variant	rs16973350
Chromosome Location	chr19:39854009-39854010
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39853890..39856826-chr19:39881619..39883140,2	MCF-7	breast:
2	chr19:39848239..39850464-chr19:39853560..39855951,2	MCF-7	breast:
3	chr19:39849660..39851695-chr19:39853601..39855209,2	K562	blood:
4	chr19:39852271..39854551-chr19:39902841..39904551,2	MCF-7	breast:
5	chr19:39845171..39847406-chr19:39852212..39854156,2	MCF-7	breast:
6	chr19:39853372..39857037-chr19:39858264..39860770,3	MCF-7	breast:
7	chr19:39834449..39837367-chr19:39853608..39855481,2	K562	blood:

Variant related genes	Relation type
ENSG00000179134	Chromatin interaction
ENSG00000241983	Chromatin interaction
ENSG00000006712	Chromatin interaction
ENSG00000090924	Chromatin interaction
ENSG00000063322	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1375910	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16973342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973348	1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[ASN][1000 genomes]
rs16973363	1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[ASN][1000 genomes]
rs16973374	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2067102	1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[ASN][1000 genomes]
rs2074852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs251906	0.83[JPT][hapmap]
rs30453	0.91[JPT][hapmap]
rs30454	0.91[JPT][hapmap]
rs30455	0.91[JPT][hapmap]
rs30457	0.91[JPT][hapmap]
rs36264	0.91[JPT][hapmap]
rs36270	0.83[JPT][hapmap]
rs3786949	1.00[JPT][hapmap]
rs3826938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3865515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40353	0.83[JPT][hapmap]
rs40441	0.91[JPT][hapmap]
rs562638	0.91[JPT][hapmap]
rs56867744	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs57411196	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57479776	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs57920235	0.97[ASN][1000 genomes]
rs58586829	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59446951	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62119691	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62119694	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62119701	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62119703	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6508860	0.91[JPT][hapmap]
rs685125	0.83[JPT][hapmap]
rs73546049	0.89[EUR][1000 genomes]
rs73546081	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73547916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs917319	0.91[JPT][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	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
2	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
3	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
4	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
5	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
6	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
7	nsv911682	chr19:39847132-39914748	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
8	nsv911683	chr19:39847132-39924129	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	185 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39834200-39859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr19:39834800-39880000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:39835800-39880200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr19:39835800-39880200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr19:39836200-39880400	Strong transcription	Primary T cells from cord blood	blood
6	chr19:39836400-39862600	Strong transcription	Duodenum Mucosa	Duodenum
7	chr19:39836600-39864000	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr19:39836600-39880400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr19:39836600-39880400	Strong transcription	Fetal Brain Female	brain
10	chr19:39837400-39880000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr19:39837600-39863600	Strong transcription	Fetal Intestine Small	intestine
12	chr19:39837800-39854400	Strong transcription	Fetal Stomach	stomach
13	chr19:39837800-39855400	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr19:39838000-39880000	Strong transcription	Brain Germinal Matrix	brain
15	chr19:39838200-39858200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:39838200-39858200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:39838200-39862600	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr19:39838600-39880400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr19:39838800-39880200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:39839000-39857600	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr19:39839000-39858200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr19:39839200-39879200	Strong transcription	Dnd41	blood
23	chr19:39841600-39880000	Strong transcription	Fetal Intestine Large	intestine
24	chr19:39841800-39855400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr19:39842000-39864200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr19:39842000-39880000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr19:39842200-39880200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:39842200-39880400	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr19:39842400-39856600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:39842400-39862400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:39842400-39880400	Strong transcription	Thymus	Thymus
32	chr19:39842600-39854600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr19:39842600-39855400	Strong transcription	Fetal Thymus	thymus
34	chr19:39842600-39880400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr19:39842800-39854600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr19:39842800-39855600	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr19:39844400-39855600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr19:39844400-39857800	Strong transcription	Fetal Lung	lung
39	chr19:39847400-39864000	Strong transcription	Primary hematopoietic stem cells	blood
40	chr19:39848200-39880000	Weak transcription	Fetal Heart	heart
41	chr19:39848400-39864200	Strong transcription	K562	blood
42	chr19:39849000-39860200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr19:39850400-39881000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr19:39851400-39854800	Genic enhancers	Brain Inferior Temporal Lobe	brain
45	chr19:39851400-39856200	Weak transcription	Fetal Brain Male	brain
46	chr19:39851400-39861000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr19:39851600-39859200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr19:39851600-39862800	Weak transcription	Small Intestine	intestine
49	chr19:39851600-39866400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr19:39851800-39859200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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