Variant report

Variant	rs5999749
Chromosome Location	chr22:22187660-22187661
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:22185084..22188761-chr22:22306127..22308519,4	K562	blood:
2	chr22:22186046..22188555-chr22:22189974..22192124,2	MCF-7	breast:
3	chr22:22121708..22124390-chr22:22186109..22187874,2	K562	blood:

Variant related genes	Relation type
ENSG00000100034	Chromatin interaction
ENSG00000100030	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1063311	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs11912377	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11913721	0.92[CEU][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13056532	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2266966	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs2266969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2283791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[EUR][1000 genomes]
rs2283793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28566555	0.80[EUR][1000 genomes]
rs28697123	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2876981	0.81[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs34550586	0.82[EUR][1000 genomes]
rs4640486	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56036797	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56227348	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56398890	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5999752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62235132	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62235149	0.84[EUR][1000 genomes]
rs6518968	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7290469	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8138075	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs8139376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs9340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs9607241	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs9607285	1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9607298	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9607320	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9610271	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs9610314	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9610328	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9610338	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9610371	0.85[ASN][1000 genomes]
rs9610374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9610375	0.82[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9610400	0.82[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs5999749	LL22NC03-86G7.1	cis	Thyroid	GTEx
rs5999749	TOP3B	cis	parietal	SCAN
rs5999749	TSSK2	cis	parietal	SCAN
rs5999749	psiTPTE22	cis	parietal	SCAN
rs5999749	LZTR1	cis	cerebellum	SCAN
rs5999749	UFD1L	cis	cerebellum	SCAN
rs5999749	LL22NC03-86G7.1	cis	Nerve Tibial	GTEx
rs5999749	DGCR6	cis	cerebellum	SCAN
rs5999749	USP18	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:22173200-22189600	Weak transcription	Brain Germinal Matrix	brain
2	chr22:22173800-22189000	Weak transcription	Fetal Thymus	thymus
3	chr22:22174000-22191800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr22:22174200-22189200	Weak transcription	Fetal Stomach	stomach
5	chr22:22174600-22189200	Weak transcription	Small Intestine	intestine
6	chr22:22174600-22189800	Weak transcription	Primary T cells from cord blood	blood
7	chr22:22174600-22191800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr22:22177200-22187800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr22:22179200-22189200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr22:22179200-22191000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr22:22179600-22189400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr22:22179600-22191600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr22:22182400-22191000	Weak transcription	HUVEC	blood vessel
14	chr22:22182600-22210400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr22:22183000-22189000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr22:22183000-22189200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr22:22183000-22189200	Weak transcription	Esophagus	oesophagus
18	chr22:22184600-22189600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr22:22185400-22200400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr22:22185600-22191000	Enhancers	Primary T cells fromperipheralblood	blood
21	chr22:22185800-22187800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr22:22186000-22187800	Strong transcription	Dnd41	blood
23	chr22:22186000-22189000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr22:22186200-22191000	Enhancers	Primary B cells from cord blood	blood
25	chr22:22186600-22187800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr22:22186600-22187800	Enhancers	HSMM	muscle
27	chr22:22186600-22187800	Genic enhancers	K562	blood
28	chr22:22186800-22188400	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr22:22186800-22191600	Weak transcription	Fetal Intestine Large	intestine
30	chr22:22187000-22187800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr22:22187000-22187800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr22:22187000-22188400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr22:22187000-22189000	Weak transcription	Brain Hippocampus Middle	brain
34	chr22:22187000-22189000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr22:22187000-22189000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr22:22187000-22189200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr22:22187000-22189200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr22:22187000-22189400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr22:22187000-22189400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr22:22187000-22189400	Weak transcription	Aorta	Aorta
41	chr22:22187000-22190800	Weak transcription	Fetal Muscle Trunk	muscle
42	chr22:22187000-22191600	Weak transcription	Fetal Brain Male	brain
43	chr22:22187000-22191800	Weak transcription	Fetal Brain Female	brain
44	chr22:22187000-22195000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr22:22187200-22188400	Weak transcription	Psoas Muscle	Psoas
46	chr22:22187200-22188600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr22:22187200-22188800	Weak transcription	GM12878-XiMat	blood
48	chr22:22187200-22189000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr22:22187200-22189000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr22:22187200-22189000	Weak transcription	Brain Anterior Caudate	brain

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