Variant report

Variant	rs17759796
Chromosome Location	chr22:22190163-22190164
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:22186046..22188555-chr22:22189974..22192124,2	MCF-7	breast:

Extended variants
information (count: 88 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10427813	1.00[ASN][1000 genomes]
rs1103229	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13515	0.89[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs1530229	1.00[ASN][1000 genomes]
rs1647705	1.00[ASN][1000 genomes]
rs1647711	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1669123	1.00[ASN][1000 genomes]
rs17759598	1.00[ASN][1000 genomes]
rs17821327	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17821500	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17821818	1.00[ASN][1000 genomes]
rs17821866	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2329886	1.00[ASN][1000 genomes]
rs238781	1.00[ASN][1000 genomes]
rs238782	1.00[ASN][1000 genomes]
rs239914	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs239915	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs239916	1.00[ASN][1000 genomes]
rs239920	1.00[ASN][1000 genomes]
rs240065	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2845458	1.00[ASN][1000 genomes]
rs28721456	1.00[ASN][1000 genomes]
rs2876980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs34239349	1.00[ASN][1000 genomes]
rs412050	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs413815	1.00[ASN][1000 genomes]
rs55649326	1.00[ASN][1000 genomes]
rs56138298	1.00[ASN][1000 genomes]
rs56226933	1.00[ASN][1000 genomes]
rs5999842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6000236	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs61757982	1.00[ASN][1000 genomes]
rs61763381	1.00[ASN][1000 genomes]
rs61763388	1.00[ASN][1000 genomes]
rs61763401	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs710171	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs710176	1.00[ASN][1000 genomes]
rs717121	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs73149918	1.00[ASN][1000 genomes]
rs73149929	1.00[ASN][1000 genomes]
rs735244	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8135616	1.00[CHB][hapmap]
rs8135758	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8136405	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8139395	1.00[ASN][1000 genomes]
rs8140233	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8142650	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs861811	1.00[ASN][1000 genomes]
rs861818	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs861820	1.00[ASN][1000 genomes]
rs861821	1.00[ASN][1000 genomes]
rs861828	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs861829	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs861831	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs861832	1.00[ASN][1000 genomes]
rs861833	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs861840	1.00[ASN][1000 genomes]
rs861841	1.00[ASN][1000 genomes]
rs861844	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs861845	1.00[ASN][1000 genomes]
rs861846	1.00[ASN][1000 genomes]
rs861850	1.00[CHB][hapmap]
rs881091	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9607194	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948603	chr22:21928916-22601814	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	422 gene(s)	inside rSNPs	diseases
2	nsv948902	chr22:21928916-22657900	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	426 gene(s)	inside rSNPs	diseases
3	nsv1063962	chr22:21939722-22934593	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	477 gene(s)	inside rSNPs	diseases
4	nsv1058617	chr22:21939922-22934454	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS 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	477 gene(s)	inside rSNPs	diseases
5	nsv529694	chr22:21957411-22905068	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases
6	nsv531797	chr22:21977700-22959729	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	476 gene(s)	inside rSNPs	diseases
7	nsv1066403	chr22:22010822-22352262	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
8	nsv1066964	chr22:22055123-22228745	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv544604	chr22:22055123-22228745	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv948580	chr22:22100718-22839559	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
11	esv1795495	chr22:22131125-22204916	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv914470	chr22:22131125-22272737	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv1059265	chr22:22131125-22457154	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	esv3379268	chr22:22135347-22446281	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	47 gene(s)	inside rSNPs	diseases
15	esv3385441	chr22:22135777-22320294	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
16	esv2752404	chr22:22141825-22570417	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
17	esv2422277	chr22:22144108-22442159	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS 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	47 gene(s)	inside rSNPs	diseases
18	esv2422295	chr22:22144108-22442159	Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
19	esv2422374	chr22:22152248-22595246	Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
20	esv2422403	chr22:22152248-23112582	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
21	nsv1062641	chr22:22157661-22367697	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
22	esv2422390	chr22:22157964-23112582	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
23	nsv914471	chr22:22165557-22272737	Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
24	esv2763701	chr22:22173533-22573987	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17759796	VPREB3	cis	parietal	SCAN
rs17759796	MOXD1	trans	lymphoblastoid	seeQTL
rs17759796	PEX26	cis	cerebellum	SCAN
rs17759796	PPM1F	cis	cerebellum	SCAN
rs17759796	psiTPTE22	cis	parietal	SCAN
rs17759796	TOP3B	cis	cerebellum	SCAN
rs17759796	YPEL1	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:22174000-22191800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr22:22174600-22191800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr22:22179200-22191000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr22:22179600-22191600	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr22:22182400-22191000	Weak transcription	HUVEC	blood vessel
6	chr22:22182600-22210400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr22:22185400-22200400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr22:22185600-22191000	Enhancers	Primary T cells fromperipheralblood	blood
9	chr22:22186200-22191000	Enhancers	Primary B cells from cord blood	blood
10	chr22:22186800-22191600	Weak transcription	Fetal Intestine Large	intestine
11	chr22:22187000-22190800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr22:22187000-22191600	Weak transcription	Fetal Brain Male	brain
13	chr22:22187000-22191800	Weak transcription	Fetal Brain Female	brain
14	chr22:22187000-22195000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr22:22187200-22190600	Weak transcription	HepG2	liver
16	chr22:22187200-22190800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr22:22187200-22191200	Weak transcription	NH-A	brain
18	chr22:22187200-22191200	Weak transcription	Osteobl	bone
19	chr22:22187200-22191400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr22:22187200-22191400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr22:22187200-22191600	Weak transcription	Liver	Liver
22	chr22:22187200-22191600	Weak transcription	Fetal Intestine Small	intestine
23	chr22:22187200-22191600	Weak transcription	Hela-S3	cervix
24	chr22:22187200-22191800	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr22:22187200-22198200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr22:22187200-22198400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr22:22187200-22200200	Weak transcription	Spleen	Spleen
28	chr22:22187400-22190800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr22:22187400-22191200	Weak transcription	HMEC	breast
30	chr22:22187400-22191600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr22:22187400-22191600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr22:22187400-22191600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr22:22187400-22191600	Weak transcription	A549	lung
34	chr22:22187600-22191800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr22:22187600-22191800	Weak transcription	HSMMtube	muscle
36	chr22:22187800-22190800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr22:22187800-22191200	Weak transcription	HSMM	muscle
38	chr22:22187800-22211000	Weak transcription	Dnd41	blood
39	chr22:22188000-22190600	Enhancers	Primary B cells from peripheral blood	blood
40	chr22:22188200-22190600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr22:22188600-22191000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr22:22188800-22190400	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr22:22189000-22190200	Enhancers	Psoas Muscle	Psoas
44	chr22:22189000-22190400	Enhancers	Brain Anterior Caudate	brain
45	chr22:22189000-22190400	Enhancers	Brain Hippocampus Middle	brain
46	chr22:22189000-22190400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr22:22189000-22190400	Enhancers	Brain Substantia Nigra	brain
48	chr22:22189000-22190400	Enhancers	Duodenum Mucosa	Duodenum
49	chr22:22189000-22190400	Enhancers	Fetal Lung	lung
50	chr22:22189000-22190600	Enhancers	Fetal Thymus	thymus

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