Variant report

Variant	rs56398890
Chromosome Location	chr22:22190785-22190786
allele	A/T
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:
2	chr22:22035151..22037450-chr22:22190171..22191825,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11912377	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11913721	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13056532	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2266966	0.82[ASN][1000 genomes]
rs2266969	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2283791	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2283793	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28697123	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28720995	0.83[ASN][1000 genomes]
rs4640486	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56036797	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56227348	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5999749	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5999752	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62235132	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6518968	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7290469	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9607285	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9607298	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9607320	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9610294	0.81[ASN][1000 genomes]
rs9610314	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9610328	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9610338	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9610371	0.88[ASN][1000 genomes]
rs9610374	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9610375	0.88[ASN][1000 genomes]
rs9610400	0.83[EUR][1000 genomes];0.85[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56398890	LL22NC03-86G7.1	cis	Nerve Tibial	GTEx

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	chr22:22187200-22190800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr22:22187200-22191200	Weak transcription	NH-A	brain
17	chr22:22187200-22191200	Weak transcription	Osteobl	bone
18	chr22:22187200-22191400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr22:22187200-22191400	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr22:22187200-22191600	Weak transcription	Liver	Liver
21	chr22:22187200-22191600	Weak transcription	Fetal Intestine Small	intestine
22	chr22:22187200-22191600	Weak transcription	Hela-S3	cervix
23	chr22:22187200-22191800	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr22:22187200-22198200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr22:22187200-22198400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr22:22187200-22200200	Weak transcription	Spleen	Spleen
27	chr22:22187400-22190800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr22:22187400-22191200	Weak transcription	HMEC	breast
29	chr22:22187400-22191600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr22:22187400-22191600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr22:22187400-22191600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr22:22187400-22191600	Weak transcription	A549	lung
33	chr22:22187600-22191800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr22:22187600-22191800	Weak transcription	HSMMtube	muscle
35	chr22:22187800-22190800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr22:22187800-22191200	Weak transcription	HSMM	muscle
37	chr22:22187800-22211000	Weak transcription	Dnd41	blood
38	chr22:22188600-22191000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr22:22189000-22191400	Enhancers	Fetal Heart	heart
40	chr22:22189000-22191600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr22:22189000-22191600	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr22:22189000-22191800	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr22:22189000-22192200	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr22:22189000-22192200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr22:22189000-22192200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr22:22189000-22192200	Enhancers	K562	blood
47	chr22:22189000-22193200	Enhancers	Colon Smooth Muscle	Colon
48	chr22:22189200-22191000	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr22:22189200-22191400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr22:22189200-22192400	Enhancers	Adipose Nuclei	Adipose

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