Variant report

Variant	rs5749082
Chromosome Location	chr22:30770603-30770604
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30770373..30773335-chr22:30781440..30783217,2	MCF-7	breast:
2	chr22:30768241..30771846-chr22:30779941..30783662,3	MCF-7	breast:
3	chr22:30744496..30747323-chr22:30770304..30772637,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF215-1	chr22:30764800-30772009	NONHSAT084775

Variant related genes	Relation type
ENSG00000099999	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10376	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10427610	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1043099	1.00[ASN][1000 genomes]
rs1046199	0.92[CEU][hapmap]
rs2108093	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2299830	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4339043	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4820008	1.00[ASN][1000 genomes]
rs4820831	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4820844	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4823085	0.98[ASN][1000 genomes]
rs5749066	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs5749078	1.00[ASN][1000 genomes]
rs5753071	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs5753080	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs5753088	0.92[ASN][1000 genomes]
rs5753111	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763923	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs5997642	0.85[CEU][hapmap]
rs737723	0.88[CEU][hapmap]
rs737950	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs740219	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs757869	0.85[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs929454	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9608904	1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9619104	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5749082	SF3A1	cis	multi-tissue	Pritchard

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30753200-30782200	Weak transcription	Stomach Mucosa	stomach
2	chr22:30753400-30771400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr22:30753400-30775200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr22:30753400-30776000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr22:30753400-30777000	Weak transcription	Aorta	Aorta
6	chr22:30753600-30771400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr22:30753600-30772600	Weak transcription	NHLF	lung
8	chr22:30753600-30772800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr22:30753600-30773000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr22:30753600-30773000	Weak transcription	Gastric	stomach
11	chr22:30753600-30773400	Weak transcription	Right Ventricle	heart
12	chr22:30753600-30775400	Weak transcription	Colon Smooth Muscle	Colon
13	chr22:30753600-30775400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr22:30753600-30776200	Weak transcription	Thymus	Thymus
15	chr22:30753600-30779200	Weak transcription	Left Ventricle	heart
16	chr22:30753600-30779400	Weak transcription	NHEK	skin
17	chr22:30753600-30779600	Weak transcription	NH-A	brain
18	chr22:30753600-30782000	Weak transcription	Colonic Mucosa	Colon
19	chr22:30753600-30782000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr22:30753600-30782200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr22:30753600-30782400	Weak transcription	Primary T cells from cord blood	blood
22	chr22:30753800-30773400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr22:30753800-30775400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr22:30754000-30771400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr22:30754000-30773400	Weak transcription	Liver	Liver
26	chr22:30754200-30772800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr22:30754200-30775400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr22:30754200-30779200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr22:30754200-30782000	Weak transcription	Fetal Brain Male	brain
30	chr22:30754400-30773400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr22:30754600-30773200	Weak transcription	Brain Angular Gyrus	brain
32	chr22:30755200-30775200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr22:30755400-30773200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr22:30759000-30772200	Weak transcription	Dnd41	blood
35	chr22:30759400-30775400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr22:30759400-30775600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr22:30759600-30773400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr22:30759600-30773600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr22:30759600-30782200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr22:30762000-30782400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr22:30762400-30771200	Weak transcription	Esophagus	oesophagus
42	chr22:30762400-30773000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr22:30762400-30773000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr22:30762400-30773000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr22:30762600-30771200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr22:30762600-30772600	Weak transcription	Fetal Intestine Large	intestine
47	chr22:30762600-30773000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr22:30762600-30773800	Weak transcription	Fetal Lung	lung
49	chr22:30762800-30771600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr22:30763200-30772800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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