Variant report

Variant	rs2299825
Chromosome Location	chr22:30813323-30813324
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	MAFF	chr22:30812671-30813455	HepG2	liver:	n/a	chr22:30812951-30812969
2	MAFK	chr22:30812498-30813501	HepG2	liver:	n/a	chr22:30812952-30812967
3	FOXA1	chr22:30812916-30813391	HepG2	liver:	n/a	chr22:30813206-30813221
4	MAFK	chr22:30812637-30813505	HepG2	liver:	n/a	chr22:30812952-30812967
5	MAFK	chr22:30812690-30813386	IMR90	lung:	n/a	chr22:30812952-30812967
6	MAFK	chr22:30812805-30813362	Hela-S3	cervix:	n/a	chr22:30812952-30812967

No.	Distal block	Cell Line	Cell type
1	chr22:30793698..30796409-chr22:30812029..30813919,3	K562	blood:
2	chr22:30812731..30815358-chr22:30815799..30818479,2	MCF-7	breast:
3	chr22:30803407..30806947-chr22:30810704..30813525,4	K562	blood:
4	chr22:30804956..30807983-chr22:30811156..30814078,3	K562	blood:
5	chr22:30811683..30814342-chr22:30815539..30819304,3	K562	blood:
6	chr22:30802321..30807877-chr22:30810760..30815440,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273350	TF binding region
RNU6-564P	TF binding region
ENSG00000249590	Chromatin interaction
ENSG00000273350	Chromatin interaction
ENSG00000100003	Chromatin interaction
ENSG00000099999	Chromatin interaction
ENSG00000222915	Chromatin interaction
ENSG00000272689	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1002189	1.00[ASW][hapmap];0.89[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1076271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1076295	0.89[CEU][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1076296	0.88[JPT][hapmap];0.80[LWK][hapmap];1.00[YRI][hapmap]
rs1076297	0.89[CEU][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1076298	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1076299	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1079227	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11705092	0.89[CEU][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11912350	0.89[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11913885	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13053375	1.00[ASW][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes]
rs13053595	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13054303	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13055431	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13056326	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13057340	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13057861	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17656850	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17657174	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17657653	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17657701	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17658238	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17730485	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17730538	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17736937	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1990268	0.89[CEU][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2229807	0.89[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2240420	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28360656	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28360657	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34367123	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34995457	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35293738	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35537171	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35711436	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35782599	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4390846	0.89[CEU][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4820005	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4820006	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4820007	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4820835	0.90[AMR][1000 genomes]
rs4820836	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4820838	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4820839	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4823089	1.00[ASW][hapmap];0.94[CEU][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56300819	0.81[AMR][1000 genomes]
rs5749062	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5749063	0.89[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5749067	0.89[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5749075	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5749076	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5749077	0.90[AMR][1000 genomes]
rs5749080	1.00[ASW][hapmap];0.84[CEU][hapmap];0.89[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5749081	1.00[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.82[CHD][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5749086	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5749087	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5749088	0.85[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5753060	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5753061	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5753069	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5753070	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5753073	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5753078	0.89[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5753082	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5753095	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5753096	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5753097	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5753101	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5753105	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5753106	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5753110	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5753113	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5753118	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs5753127	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5763928	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.80[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs5763932	0.84[AMR][1000 genomes]
rs61322750	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62228968	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7284531	0.88[JPT][hapmap]
rs7287175	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7287908	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7288947	0.89[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs737750	1.00[ASW][hapmap];0.88[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs737751	1.00[ASW][hapmap];0.89[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs737813	0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs737948	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.80[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs740084	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs740220	0.89[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs740222	0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs740223	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs757868	0.89[CEU][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8136826	0.84[AMR][1000 genomes];0.85[EUR][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2299825	RP1-130H16.16	cis	lung	GTEx
rs2299825	CABP7	cis	cerebellum	SCAN
rs2299825	CHEK2	cis	cerebellum	SCAN
rs2299825	RP1-130H16.16	cis	Thyroid	GTEx
rs2299825	NIPSNAP1	cis	cerebellum	SCAN
rs2299825	RNF215	cis	Heart Left Ventricle	GTEx
rs2299825	C22orf42	cis	cerebellum	SCAN
rs2299825	CRYBB3	cis	cerebellum	SCAN
rs2299825	NEFH	cis	parietal	SCAN
rs2299825	SEC14L2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30794000-30816600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr22:30794000-30818000	Weak transcription	Right Atrium	heart
3	chr22:30794800-30818600	Weak transcription	Primary B cells from cord blood	blood
4	chr22:30795000-30814600	Weak transcription	Colon Smooth Muscle	Colon
5	chr22:30795200-30814400	Weak transcription	Small Intestine	intestine
6	chr22:30796000-30813400	Weak transcription	Fetal Kidney	kidney
7	chr22:30797800-30816400	Strong transcription	Dnd41	blood
8	chr22:30799400-30817600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr22:30801200-30814400	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr22:30801400-30816600	Strong transcription	Fetal Stomach	stomach
11	chr22:30802000-30816400	Strong transcription	Stomach Smooth Muscle	stomach
12	chr22:30802200-30816200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr22:30802200-30817000	Genic enhancers	Liver	Liver
14	chr22:30802600-30814800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr22:30803200-30814000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr22:30803200-30817200	Strong transcription	Fetal Muscle Trunk	muscle
17	chr22:30803400-30815200	Strong transcription	Brain Substantia Nigra	brain
18	chr22:30804800-30815600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr22:30805000-30818200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr22:30805200-30816400	Weak transcription	NHDF-Ad	bronchial
21	chr22:30805800-30816200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr22:30805800-30816200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr22:30806600-30815600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr22:30807000-30816200	Strong transcription	Brain Hippocampus Middle	brain
25	chr22:30808400-30815200	Strong transcription	Thymus	Thymus
26	chr22:30808400-30817400	Strong transcription	Fetal Muscle Leg	muscle
27	chr22:30808800-30815200	Strong transcription	NH-A	brain
28	chr22:30809000-30815200	Strong transcription	Fetal Lung	lung
29	chr22:30809000-30815200	Strong transcription	NHLF	lung
30	chr22:30809000-30818200	Strong transcription	Fetal Brain Female	brain
31	chr22:30809800-30818400	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr22:30809800-30818400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr22:30810000-30817800	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr22:30810200-30815600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr22:30810400-30816400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr22:30810600-30815400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr22:30810600-30817800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr22:30810800-30815000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr22:30810800-30815200	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr22:30810800-30815400	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr22:30810800-30815800	Strong transcription	HSMM	muscle
42	chr22:30810800-30816400	Weak transcription	Fetal Heart	heart
43	chr22:30811000-30814200	Strong transcription	Brain Cingulate Gyrus	brain
44	chr22:30811000-30814800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr22:30811000-30815400	Strong transcription	Brain Angular Gyrus	brain
46	chr22:30811000-30818000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr22:30811200-30817000	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr22:30811400-30813400	Strong transcription	Pancreas	Pancrea
49	chr22:30811400-30813800	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr22:30811400-30814000	Strong transcription	Right Ventricle	heart

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