Variant report

Variant	rs1110295
Chromosome Location	chr3:49880943-49880944
allele	C/T
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	USF1	chr3:49880301-49880991	H1-hESC	embryonic stem cell:	n/a	chr3:49880518-49880529
2	USF2	chr3:49880663-49880951	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49709674..49711782-chr3:49878880..49881379,2	K562	blood:

Variant related genes	Relation type
TRAIP	TF binding region
ENSG00000164062	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17050885	1.00[AMR][1000 genomes]
rs17050913	1.00[AMR][1000 genomes]
rs17050922	1.00[AMR][1000 genomes]
rs59325781	1.00[AMR][1000 genomes]
rs61689372	1.00[AMR][1000 genomes]
rs72936049	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936059	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938108	0.82[AFR][1000 genomes]
rs72938138	0.80[AFR][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	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1110295	MAPKAPK3	cis	lymphoblastoid	seeQTL
rs1110295	HEMK	cis	multi-tissue	Pritchard

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49861200-49882200	Weak transcription	Primary B cells from cord blood	blood
2	chr3:49861200-49893200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:49863800-49882800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr3:49864000-49883200	Weak transcription	Colonic Mucosa	Colon
5	chr3:49864000-49893200	Weak transcription	Placenta	Placenta
6	chr3:49864200-49893000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:49864600-49882000	Weak transcription	Osteobl	bone
8	chr3:49864800-49886000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:49865000-49886000	Strong transcription	Dnd41	blood
10	chr3:49865600-49885800	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:49865600-49885800	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:49866000-49881000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:49869000-49883200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:49869200-49881000	Weak transcription	HMEC	breast
15	chr3:49869400-49893000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr3:49870200-49893000	Weak transcription	HSMM	muscle
17	chr3:49871200-49886000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:49873600-49885800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:49873800-49885800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:49874000-49885800	Strong transcription	Thymus	Thymus
21	chr3:49874800-49882000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:49876000-49881800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:49876000-49882800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr3:49876600-49881200	Enhancers	Fetal Heart	heart
25	chr3:49877000-49882400	Weak transcription	Primary B cells from peripheral blood	blood
26	chr3:49877000-49893000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr3:49877000-49893400	Weak transcription	HSMMtube	muscle
28	chr3:49877200-49882200	Weak transcription	Brain Germinal Matrix	brain
29	chr3:49877200-49885000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:49877200-49886000	Weak transcription	Stomach Mucosa	stomach
31	chr3:49877200-49893000	Weak transcription	Gastric	stomach
32	chr3:49877200-49893000	Weak transcription	NHDF-Ad	bronchial
33	chr3:49877200-49893200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:49877400-49881800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:49877400-49882600	Weak transcription	Ovary	ovary
36	chr3:49877400-49883000	Weak transcription	Liver	Liver
37	chr3:49877400-49883000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:49877400-49893000	Weak transcription	A549	lung
39	chr3:49877400-49893200	Weak transcription	Lung	lung
40	chr3:49877400-49893200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr3:49877600-49893200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr3:49877800-49885800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr3:49877800-49893000	Weak transcription	Esophagus	oesophagus
44	chr3:49877800-49893000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr3:49878000-49883800	Weak transcription	Colon Smooth Muscle	Colon
46	chr3:49878000-49886000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:49878200-49884000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr3:49878400-49885800	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr3:49878600-49881600	Genic enhancers	HepG2	liver
50	chr3:49878600-49883800	Weak transcription	Fetal Lung	lung

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