Variant report

Variant	rs1079227
Chromosome Location	chr22:30699128-30699129
allele	C/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	SPI1	chr22:30698262-30699159	GM12878	blood:	n/a	chr22:30698744-30698757 chr22:30698680-30698687 chr22:30698746-30698755 chr22:30698743-30698756

No.	Distal block	Cell Line	Cell type
1	chr22:30698626..30701089-chr22:30721523..30724140,3	MCF-7	breast:
2	chr22:30698659..30701498-chr22:30769224..30771586,2	MCF-7	breast:
3	chr22:30689707..30691265-chr22:30696967..30699657,2	K562	blood:
4	chr22:30697290..30700187-chr22:30735084..30737167,2	MCF-7	breast:
5	chr22:30697815..30699936-chr22:30705927..30707445,2	K562	blood:

Variant related genes	Relation type
ENSG00000248751	TF binding region
TBC1D10A	TF binding region
ENSG00000187860	Chromatin interaction
ENSG00000099995	Chromatin interaction
ENSG00000099992	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1002189	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1076271	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1076295	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1076296	0.88[ASN][1000 genomes]
rs1076297	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1076298	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1076299	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11705092	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11912350	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11913885	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13053375	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13053595	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13054303	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13055431	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13056253	0.98[ASN][1000 genomes]
rs13056326	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13057340	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13057861	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17656850	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17657174	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17657653	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17657701	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17658238	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17730485	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17730538	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17736937	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1990268	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2097919	0.84[AFR][1000 genomes]
rs2229807	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2240420	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2299825	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28360656	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34367123	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34995457	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35293738	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35537171	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35711436	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35782599	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4390846	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4820005	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4820006	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4820007	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4820835	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4820836	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4820838	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4820839	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4823089	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55979575	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56300819	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5749062	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5749063	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5749067	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5749075	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5749076	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5749077	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5749080	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5749081	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5749086	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5749087	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5749088	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5753058	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753060	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753061	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753069	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753070	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753073	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753078	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753082	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753095	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753096	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753097	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753101	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5753105	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5753106	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5753110	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5753113	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5753127	0.86[AMR][1000 genomes]
rs5763928	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5763932	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763939	0.81[AFR][1000 genomes]
rs61322750	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62228968	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7284531	0.98[ASN][1000 genomes]
rs7287175	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7287908	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7288947	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs737750	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs737751	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs737813	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs737948	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs740084	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs740220	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs740222	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs740223	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs757868	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8136826	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv834174	chr22:30619760-30746915	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS 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 target site	24 gene(s)	inside rSNPs	diseases
4	nsv1062388	chr22:30649179-30711443	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv984527	chr22:30698358-30732712	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1079227	RNF215	cis	Heart Left Ventricle	GTEx
rs1079227	RP1-130H16.16	cis	lung	GTEx
rs1079227	RP1-130H16.16	cis	Thyroid	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30686000-30700000	Weak transcription	Fetal Kidney	kidney
2	chr22:30686200-30720000	Weak transcription	Fetal Brain Male	brain
3	chr22:30686400-30701800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr22:30686600-30700600	Genic enhancers	Fetal Thymus	thymus
5	chr22:30686800-30701800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr22:30686800-30707200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr22:30687000-30699600	Strong transcription	Fetal Brain Female	brain
8	chr22:30687400-30701200	Weak transcription	K562	blood
9	chr22:30687400-30706800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr22:30687600-30699800	Genic enhancers	Esophagus	oesophagus
11	chr22:30687600-30701400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr22:30688200-30699200	Strong transcription	Aorta	Aorta
13	chr22:30688200-30700600	Strong transcription	Fetal Stomach	stomach
14	chr22:30690200-30700200	Genic enhancers	Primary T cells fromperipheralblood	blood
15	chr22:30690400-30700800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr22:30690800-30699800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr22:30690800-30701600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr22:30691000-30706800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr22:30692800-30700600	Genic enhancers	Placenta	Placenta
20	chr22:30693200-30701000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr22:30693400-30701800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr22:30694400-30700200	Genic enhancers	Primary B cells from peripheral blood	blood
23	chr22:30694800-30700600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr22:30695200-30700400	Genic enhancers	Spleen	Spleen
25	chr22:30695400-30701000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr22:30695400-30706800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr22:30696200-30699200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
28	chr22:30696400-30700400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr22:30696400-30700400	Genic enhancers	Adipose Nuclei	Adipose
30	chr22:30696400-30701000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr22:30696400-30701200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr22:30696400-30703200	Enhancers	Brain Hippocampus Middle	brain
33	chr22:30696400-30703200	Enhancers	Placenta Amnion	Placenta Amnion
34	chr22:30696600-30700400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr22:30696600-30700800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr22:30696600-30701000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr22:30696600-30701000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr22:30696600-30702400	Enhancers	Right Atrium	heart
39	chr22:30696800-30699800	Genic enhancers	Fetal Muscle Leg	muscle
40	chr22:30696800-30700400	Strong transcription	Brain Germinal Matrix	brain
41	chr22:30696800-30700800	Genic enhancers	Stomach Smooth Muscle	stomach
42	chr22:30697000-30699600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr22:30697000-30699600	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr22:30697000-30699800	Genic enhancers	Stomach Mucosa	stomach
45	chr22:30697000-30703600	Enhancers	Brain Substantia Nigra	brain
46	chr22:30697200-30699200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr22:30697200-30699600	Genic enhancers	HSMMtube	muscle
48	chr22:30697200-30700000	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr22:30697200-30700400	Genic enhancers	Rectal Mucosa Donor 31	rectum
50	chr22:30697200-30700800	Genic enhancers	Gastric	stomach

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