Variant report

Variant	rs17657701
Chromosome Location	chr22:30753985-30753986
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30692983..30695862-chr22:30751814..30754169,4	MCF-7	breast:
2	chr22:30684284..30686749-chr22:30752450..30754272,3	MCF-7	breast:
3	chr22:30722006..30725049-chr22:30749886..30754508,5	K562	blood:
4	chr22:30736285..30738437-chr22:30751447..30754136,2	K562	blood:
5	chr22:30720936..30724991-chr22:30750350..30754449,10	MCF-7	breast:
6	chr22:30679588..30687274-chr22:30748772..30756086,11	MCF-7	breast:
7	chr22:30681963..30685470-chr22:30751422..30755510,6	K562	blood:
8	chr22:30689967..30692152-chr22:30752675..30754508,2	MCF-7	breast:
9	chr22:30719395..30724233-chr22:30750032..30754717,7	MCF-7	breast:
10	chr22:30681129..30691076-chr22:30751303..30759078,14	K562	blood:
11	chr22:30736285..30738543-chr22:30751447..30754136,3	K562	blood:
12	chr22:30732348..30737677-chr22:30750921..30755238,7	MCF-7	breast:
13	chr22:30712771..30715254-chr22:30752580..30754854,2	MCF-7	breast:
14	chr22:30722006..30724246-chr22:30752442..30754508,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000099992	Chromatin interaction
ENSG00000239282	Chromatin interaction
ENSG00000099995	Chromatin interaction
ENSG00000248751	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1002189	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1076271	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1076295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1076296	0.94[ASN][1000 genomes]
rs1076297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1076298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1076299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1079227	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11705092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11912350	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11913885	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13053375	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13053595	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13054303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13055431	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13056253	0.89[ASN][1000 genomes]
rs13056326	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13057340	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13057861	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17656850	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17657174	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17657653	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17658238	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17730485	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17730538	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17736937	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1990268	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2229807	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2240420	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2299825	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28360656	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34367123	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34995457	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35289401	0.83[ASN][1000 genomes]
rs35293738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35537171	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35711436	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35782599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4390846	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4820005	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4820006	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4820007	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4820835	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4820836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4820838	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4820839	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4823089	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55979575	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56300819	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5749062	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5749063	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5749067	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5749075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5749076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5749077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5749080	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5749081	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5749086	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5749087	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5749088	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5753058	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5753060	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753061	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753069	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753070	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753073	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753078	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753082	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5753096	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5753097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5753101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5753105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5753106	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5753110	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753113	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5753127	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5763928	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763932	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59731356	0.83[ASN][1000 genomes]
rs5997623	0.85[AFR][1000 genomes]
rs61322750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62228968	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7284531	0.89[ASN][1000 genomes]
rs7287175	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7287908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7288947	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs737750	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs737751	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs737813	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs737948	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs740084	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs740220	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs740222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs740223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs757868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8136826	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9608885	0.88[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	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
4	nsv1066179	chr22:30724148-30766466	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17657701	RP1-130H16.16	cis	Thyroid	GTEx
rs17657701	RP1-130H16.16	cis	Esophagus Muscularis	GTEx
rs17657701	RNF215	cis	Heart Left Ventricle	GTEx
rs17657701	RP1-130H16.16	cis	Artery Aorta	GTEx
rs17657701	RP1-130H16.16	cis	lung	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30750600-30754400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr22:30751400-30754000	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr22:30751400-30754200	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr22:30751600-30754000	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr22:30751600-30754200	Active TSS	H9 Cell Line	embryonic stem cell
6	chr22:30751600-30754200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr22:30751800-30754000	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr22:30751800-30754200	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr22:30752000-30754000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr22:30752200-30754000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr22:30752800-30754200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr22:30752800-30754400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr22:30753200-30782200	Weak transcription	Stomach Mucosa	stomach
14	chr22:30753400-30754000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr22:30753400-30754000	Enhancers	Spleen	Spleen
16	chr22:30753400-30754200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr22:30753400-30761600	Weak transcription	Esophagus	oesophagus
18	chr22:30753400-30771400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr22:30753400-30775200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr22:30753400-30776000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr22:30753400-30777000	Weak transcription	Aorta	Aorta
22	chr22:30753600-30754000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr22:30753600-30754000	Enhancers	Adipose Nuclei	Adipose
24	chr22:30753600-30754000	Enhancers	Liver	Liver
25	chr22:30753600-30754000	Enhancers	HMEC	breast
26	chr22:30753600-30754200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr22:30753600-30754200	Enhancers	Primary T cells fromperipheralblood	blood
28	chr22:30753600-30754200	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr22:30753600-30754200	Weak transcription	Brain Angular Gyrus	brain
30	chr22:30753600-30754200	Active TSS	Brain Anterior Caudate	brain
31	chr22:30753600-30754200	Enhancers	Brain Cingulate Gyrus	brain
32	chr22:30753600-30754200	Enhancers	Fetal Brain Male	brain
33	chr22:30753600-30754200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
34	chr22:30753600-30754200	Bivalent Enhancer	Fetal Muscle Leg	muscle
35	chr22:30753600-30754200	Enhancers	Fetal Thymus	thymus
36	chr22:30753600-30754200	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr22:30753600-30754200	Enhancers	Stomach Smooth Muscle	stomach
38	chr22:30753600-30754200	Enhancers	K562	blood
39	chr22:30753600-30754600	Enhancers	Dnd41	blood
40	chr22:30753600-30754800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr22:30753600-30755200	Enhancers	Fetal Intestine Large	intestine
42	chr22:30753600-30755400	Weak transcription	Fetal Stomach	stomach
43	chr22:30753600-30758200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr22:30753600-30758600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr22:30753600-30758600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr22:30753600-30761600	Weak transcription	Lung	lung
47	chr22:30753600-30761800	Weak transcription	Fetal Lung	lung
48	chr22:30753600-30762000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr22:30753600-30765800	Weak transcription	Fetal Kidney	kidney
50	chr22:30753600-30765800	Weak transcription	Pancreas	Pancrea

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