Variant report

Variant	rs73930679
Chromosome Location	chr19:40481293-40481294
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	chr19:40472172-40495393	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:40441756..40443271-chr19:40480700..40482309,2	K562	blood:
2	chr19:40472468..40476413-chr19:40479730..40482224,3	MCF-7	breast:
3	chr19:40473089..40482317-chr19:40483091..40492558,21	K562	blood:

Variant related genes	Relation type
PSMC4	TF binding region
ENSG00000013275	Chromatin interaction
ENSG00000187187	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10403646	1.00[AMR][1000 genomes]
rs10410695	1.00[EUR][1000 genomes]
rs10418448	1.00[EUR][1000 genomes]
rs10419218	1.00[EUR][1000 genomes]
rs10420514	1.00[EUR][1000 genomes]
rs10420687	1.00[EUR][1000 genomes]
rs10421243	1.00[EUR][1000 genomes]
rs10423298	1.00[EUR][1000 genomes]
rs10423800	1.00[EUR][1000 genomes]
rs10427117	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11883159	1.00[EUR][1000 genomes]
rs13382054	1.00[EUR][1000 genomes]
rs170898	1.00[EUR][1000 genomes]
rs234297	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234307	1.00[EUR][1000 genomes]
rs234312	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234316	1.00[EUR][1000 genomes]
rs234319	1.00[EUR][1000 genomes]
rs234321	1.00[EUR][1000 genomes]
rs234322	1.00[EUR][1000 genomes]
rs234327	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234339	1.00[EUR][1000 genomes]
rs234342	1.00[EUR][1000 genomes]
rs2542302	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28661993	1.00[EUR][1000 genomes]
rs28776318	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28832070	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs337795	1.00[EUR][1000 genomes]
rs57342065	1.00[EUR][1000 genomes]
rs58348431	1.00[EUR][1000 genomes]
rs59707868	1.00[EUR][1000 genomes]
rs60631264	1.00[EUR][1000 genomes]
rs61424085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7245930	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7250945	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7257627	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7258111	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7258718	1.00[AMR][1000 genomes]
rs73930675	1.00[EUR][1000 genomes]
rs73930678	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8111518	1.00[EUR][1000 genomes]
rs8111741	1.00[EUR][1000 genomes]
rs9630860	1.00[EUR][1000 genomes]
rs9630868	1.00[EUR][1000 genomes]
rs9783944	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer 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	43 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	chr19:40477800-40501800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:40478000-40485600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:40478200-40481400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:40478200-40481600	Strong transcription	Rectal Smooth Muscle	rectum
5	chr19:40478200-40481800	Strong transcription	Primary T cells from cord blood	blood
6	chr19:40478200-40482000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:40478200-40482000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr19:40478200-40482200	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr19:40478200-40482200	Strong transcription	Fetal Lung	lung
10	chr19:40478200-40488200	Strong transcription	Thymus	Thymus
11	chr19:40478200-40488400	Strong transcription	Fetal Stomach	stomach
12	chr19:40478200-40489200	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr19:40478200-40489200	Strong transcription	Primary B cells from cord blood	blood
14	chr19:40478200-40489400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr19:40478200-40489400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr19:40478200-40489600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:40478400-40481400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr19:40478400-40481400	Strong transcription	A549	lung
19	chr19:40478400-40481600	Strong transcription	Colonic Mucosa	Colon
20	chr19:40478400-40481800	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr19:40478400-40481800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
22	chr19:40478400-40481800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr19:40478400-40481800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr19:40478400-40481800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:40478400-40481800	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr19:40478400-40481800	Strong transcription	Brain Cingulate Gyrus	brain
27	chr19:40478400-40481800	Strong transcription	Duodenum Mucosa	Duodenum
28	chr19:40478400-40481800	Strong transcription	Fetal Thymus	thymus
29	chr19:40478400-40481800	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr19:40478400-40481800	Strong transcription	HUVEC	blood vessel
31	chr19:40478400-40481800	Strong transcription	NHEK	skin
32	chr19:40478400-40481800	Strong transcription	NHLF	lung
33	chr19:40478400-40482000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr19:40478400-40482000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:40478400-40482000	Strong transcription	Brain Hippocampus Middle	brain
36	chr19:40478400-40482000	Strong transcription	Brain Substantia Nigra	brain
37	chr19:40478400-40482000	Strong transcription	Fetal Intestine Large	intestine
38	chr19:40478400-40482000	Strong transcription	Placenta	Placenta
39	chr19:40478400-40482000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr19:40478400-40482000	Strong transcription	HMEC	breast
41	chr19:40478400-40482000	Strong transcription	Osteobl	bone
42	chr19:40478400-40482200	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr19:40478400-40482200	Strong transcription	Primary B cells from peripheral blood	blood
44	chr19:40478400-40482200	Strong transcription	Spleen	Spleen
45	chr19:40478400-40482400	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr19:40478400-40488000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:40478400-40488200	Strong transcription	Fetal Muscle Trunk	muscle
48	chr19:40478400-40488200	Strong transcription	Fetal Muscle Leg	muscle
49	chr19:40478400-40488400	Strong transcription	Brain Anterior Caudate	brain
50	chr19:40478400-40488800	Strong transcription	HUES64 Cell Line	embryonic stem cell

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