Variant report

Variant	rs73549931
Chromosome Location	chr19:39944936-39944937
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39944762-39945190	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39935025..39939391-chr19:39941670..39945820,7	MCF-7	breast:
2	chr19:39944081..39946194-chr19:39971487..39974078,2	MCF-7	breast:

Variant related genes	Relation type
SUPT5H	TF binding region
ENSG00000196235	Chromatin interaction
ENSG00000105197	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10413140	1.00[AMR][1000 genomes]
rs13346052	1.00[AMR][1000 genomes]
rs61569178	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73547970	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73547976	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73547991	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73547993	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73547999	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549905	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549906	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549922	1.00[AMR][1000 genomes]
rs73549928	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551806	1.00[AMR][1000 genomes]
rs73551815	1.00[AMR][1000 genomes]
rs73551829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551844	1.00[AMR][1000 genomes]
rs7359872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
2	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	esv1791966	chr19:39921479-39954931	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
6	nsv544003	chr19:39937078-39974282	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39936800-39949200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:39937000-39949000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:39937000-39971000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:39937400-39971000	Weak transcription	Right Atrium	heart
5	chr19:39937600-39946000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr19:39937600-39950000	Weak transcription	Fetal Brain Male	brain
7	chr19:39937800-39946200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:39938600-39967600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:39938800-39946400	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr19:39939000-39946000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:39939000-39950000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr19:39939000-39953400	Strong transcription	Fetal Intestine Small	intestine
13	chr19:39939200-39948800	Weak transcription	Stomach Mucosa	stomach
14	chr19:39939200-39967600	Strong transcription	Fetal Thymus	thymus
15	chr19:39939400-39945400	Weak transcription	HSMMtube	muscle
16	chr19:39939400-39945800	Strong transcription	Fetal Muscle Leg	muscle
17	chr19:39939400-39946000	Strong transcription	Lung	lung
18	chr19:39939400-39946000	Strong transcription	NHEK	skin
19	chr19:39939400-39968800	Strong transcription	Fetal Stomach	stomach
20	chr19:39940000-39945800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr19:39940000-39945800	Strong transcription	Brain Cingulate Gyrus	brain
22	chr19:39940000-39948000	Weak transcription	Psoas Muscle	Psoas
23	chr19:39940000-39950400	Weak transcription	Small Intestine	intestine
24	chr19:39940000-39952200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr19:39940000-39968000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr19:39940200-39968600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:39940200-39968600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr19:39940200-39968800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:39940200-39970600	Weak transcription	Fetal Heart	heart
30	chr19:39940400-39946200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr19:39940400-39949000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr19:39941000-39945800	Strong transcription	A549	lung
33	chr19:39941000-39951800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr19:39941200-39949200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr19:39941200-39952800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr19:39941200-39953200	Strong transcription	Dnd41	blood
37	chr19:39941200-39954200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr19:39941400-39952200	Strong transcription	Fetal Brain Female	brain
39	chr19:39941400-39967400	Strong transcription	Fetal Intestine Large	intestine
40	chr19:39941600-39947400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr19:39942000-39945800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr19:39942000-39945800	Strong transcription	K562	blood
43	chr19:39942000-39946200	Strong transcription	Primary T cells from cord blood	blood
44	chr19:39942000-39967400	Strong transcription	Thymus	Thymus
45	chr19:39942000-39967600	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr19:39942200-39945800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr19:39942200-39945800	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr19:39942200-39945800	Strong transcription	Brain Anterior Caudate	brain
49	chr19:39942200-39945800	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr19:39942200-39946000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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