Variant report

Variant	rs5999550
Chromosome Location	chr22:22151286-22151287
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:22145100..22147848-chr22:22150073..22153160,3	K562	blood:
2	chr22:22150579..22153553-chr22:22290936..22295210,3	K562	blood:
3	chr22:22149608..22152271-chr22:22219755..22223079,3	MCF-7	breast:
4	chr22:22149149..22152103-chr22:22281667..22284130,2	K562	blood:
5	chr22:22139542..22142043-chr22:22149818..22151655,3	K562	blood:
6	chr22:22144744..22147621-chr22:22148785..22151318,2	K562	blood:
7	chr22:22139792..22142043-chr22:22150140..22151655,2	K562	blood:

Variant related genes	Relation type
ENSG00000224086	Chromatin interaction
ENSG00000100030	Chromatin interaction
ENSG00000100034	Chromatin interaction
ENSG00000200985	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11704205	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13943	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1892846	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1892848	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2006893	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2266965	0.80[EUR][1000 genomes]
rs2266967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2283792	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2283794	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2298432	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs240049	0.89[CEU][hapmap]
rs28566555	0.84[EUR][1000 genomes]
rs34550586	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3788332	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3810609	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3810610	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4478016	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4516540	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4821402	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5749806	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5749937	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5749986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5749998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5750113	0.96[CEU][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5755099	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5755654	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5755694	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5999515	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5999521	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5999750	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6518986	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6928	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs743409	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8136590	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8136867	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8141851	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9607287	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9607340	0.84[EUR][1000 genomes]
rs9607347	0.88[EUR][1000 genomes]
rs9610375	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs9610458	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9610500	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	nsv588322	chr22:22086373-22186479	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs5999550	LL22NC03-86G7.1	cis	Skin Sun Exposed Lower leg	GTEx
rs5999550	LL22NC03-86G7.1	cis	Heart Left Ventricle	GTEx
rs5999550	LL22NC03-86G7.1	cis	Muscle Skeletal	GTEx
rs5999550	MAPK1	Cis_1M	lymphoblastoid	RTeQTL
rs5999550	LL22NC03-86G7.1	cis	Thyroid	GTEx
rs5999550	LL22NC03-86G7.1	cis	Adipose Subcutaneous	GTEx
rs5999550	LL22NC03-86G7.1	cis	Whole Blood	GTEx
rs5999550	PPM1F	cis	uninvolved skin	skin_eQTL
rs5999550	LL22NC03-86G7.1	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:22113400-22163800	Weak transcription	Right Atrium	heart
2	chr22:22114200-22172800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr22:22121600-22171400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr22:22123200-22162200	Strong transcription	Fetal Thymus	thymus
5	chr22:22127200-22167600	Weak transcription	Psoas Muscle	Psoas
6	chr22:22127200-22170600	Weak transcription	Hela-S3	cervix
7	chr22:22129000-22162200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr22:22129800-22152000	Weak transcription	Brain Germinal Matrix	brain
9	chr22:22132000-22152000	Weak transcription	Right Ventricle	heart
10	chr22:22133400-22156000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr22:22134200-22162200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr22:22135200-22152400	Strong transcription	Fetal Muscle Trunk	muscle
13	chr22:22135200-22162200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr22:22135800-22162400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr22:22135800-22162600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:22135800-22162600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr22:22136000-22162400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr22:22136200-22161800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr22:22137600-22152400	Weak transcription	Esophagus	oesophagus
20	chr22:22137600-22162600	Strong transcription	Dnd41	blood
21	chr22:22138400-22152000	Weak transcription	Spleen	Spleen
22	chr22:22139200-22172800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr22:22139400-22151800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr22:22139600-22154600	Weak transcription	Fetal Brain Male	brain
25	chr22:22140800-22161800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr22:22141000-22162000	Strong transcription	Fetal Intestine Large	intestine
27	chr22:22141000-22162200	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr22:22142800-22170600	Weak transcription	Colonic Mucosa	Colon
29	chr22:22143200-22152400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr22:22143200-22155000	Weak transcription	Aorta	Aorta
31	chr22:22144000-22154400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr22:22144200-22151400	Strong transcription	Fetal Stomach	stomach
33	chr22:22144400-22160200	Strong transcription	Fetal Intestine Small	intestine
34	chr22:22145200-22162200	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr22:22145600-22152000	Weak transcription	Left Ventricle	heart
36	chr22:22145800-22170600	Weak transcription	Small Intestine	intestine
37	chr22:22146000-22162000	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr22:22146200-22152000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr22:22146200-22152200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr22:22146400-22162200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr22:22146600-22151800	Weak transcription	Stomach Mucosa	stomach
42	chr22:22146600-22151800	Weak transcription	GM12878-XiMat	blood
43	chr22:22146600-22152200	Weak transcription	HSMMtube	muscle
44	chr22:22146600-22152200	Weak transcription	NH-A	brain
45	chr22:22146600-22152400	Weak transcription	NHLF	lung
46	chr22:22146600-22153200	Weak transcription	A549	lung
47	chr22:22146600-22154200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr22:22146800-22154400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr22:22147200-22152200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr22:22147200-22154000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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