Variant report

Variant	rs5999515
Chromosome Location	chr22:22145101-22145102
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:22144666-22145786	K562	blood:	n/a	n/a
2	POLR2A	chr22:22144752-22145291	K562	blood:	n/a	n/a
3	GATA1	chr22:22144071-22147721	K562	blood:	n/a	chr22:22144744-22144751
4	JUN	chr22:22143978-22146964	K562	blood:	n/a	n/a
5	POLR2A	chr22:22144704-22145454	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:22143176..22145767-chr22:22180225..22183030,2	K562	blood:
2	chr22:22145076..22147580-chr22:22220741..22222619,2	K562	blood:
3	chr22:22066653..22068423-chr22:22143403..22146205,2	K562	blood:
4	chr22:22020107..22022077-chr22:22144691..22146337,2	K562	blood:

Variant related genes	Relation type
RNA5SP493	TF binding region
ENSG00000100023	Chromatin interaction
ENSG00000100030	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11704205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1892846	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1892848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2006893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2266965	0.80[EUR][1000 genomes]
rs2266967	0.81[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2283792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2283794	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2298432	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs240049	0.89[CEU][hapmap]
rs28566555	0.84[EUR][1000 genomes]
rs34550586	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3788332	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3810609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3810610	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4478016	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4516540	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4821402	1.00[CEU][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes]
rs5749806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5749937	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5749986	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5749998	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5750113	0.81[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5754941	0.85[ASN][1000 genomes]
rs5755099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5755654	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5755694	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5999521	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5999550	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]
rs5999750	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6518986	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs743409	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8136590	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8136867	0.81[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8141851	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9607287	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9607340	0.84[EUR][1000 genomes]
rs9607347	0.88[EUR][1000 genomes]
rs9610375	0.96[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs9610458	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9610500	0.83[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs5999515	LL22NC03-86G7.1	cis	Skin Sun Exposed Lower leg	GTEx
rs5999515	LL22NC03-86G7.1	cis	Muscle Skeletal	GTEx
rs5999515	DERL3	cis	cerebellum	SCAN
rs5999515	PPM1F	cis	uninvolved skin	skin_eQTL
rs5999515	SCARF2	cis	parietal	SCAN
rs5999515	LL22NC03-86G7.1	cis	Thyroid	GTEx
rs5999515	MIF	cis	parietal	SCAN
rs5999515	LL22NC03-86G7.1	cis	Nerve Tibial	GTEx
rs5999515	LL22NC03-86G7.1	cis	Adipose Subcutaneous	GTEx
rs5999515	psiTPTE22	cis	parietal	SCAN
rs5999515	LL22NC03-86G7.1	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:22110600-22150600	Weak transcription	Fetal Heart	heart
2	chr22:22113400-22163800	Weak transcription	Right Atrium	heart
3	chr22:22114200-22172800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr22:22121600-22171400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr22:22123200-22162200	Strong transcription	Fetal Thymus	thymus
6	chr22:22127200-22145200	Weak transcription	Small Intestine	intestine
7	chr22:22127200-22146000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr22:22127200-22167600	Weak transcription	Psoas Muscle	Psoas
9	chr22:22127200-22170600	Weak transcription	Hela-S3	cervix
10	chr22:22127400-22145800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr22:22127400-22146000	Weak transcription	A549	lung
12	chr22:22129000-22162200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr22:22129600-22151200	Weak transcription	Colon Smooth Muscle	Colon
14	chr22:22129800-22152000	Weak transcription	Brain Germinal Matrix	brain
15	chr22:22130000-22150600	Weak transcription	Ovary	ovary
16	chr22:22130000-22150800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr22:22130400-22147000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr22:22131400-22150600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr22:22132000-22152000	Weak transcription	Right Ventricle	heart
20	chr22:22133400-22156000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr22:22134200-22162200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr22:22134600-22151200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr22:22135000-22146400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr22:22135200-22152400	Strong transcription	Fetal Muscle Trunk	muscle
25	chr22:22135200-22162200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr22:22135800-22162400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr22:22135800-22162600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr22:22135800-22162600	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr22:22136000-22162400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr22:22136200-22161800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr22:22136600-22146400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr22:22137600-22148200	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr22:22137600-22152400	Weak transcription	Esophagus	oesophagus
34	chr22:22137600-22162600	Strong transcription	Dnd41	blood
35	chr22:22138000-22150800	Weak transcription	Gastric	stomach
36	chr22:22138400-22152000	Weak transcription	Spleen	Spleen
37	chr22:22138800-22149400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr22:22139000-22145400	Strong transcription	GM12878-XiMat	blood
39	chr22:22139200-22145600	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr22:22139200-22172800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr22:22139400-22151800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr22:22139600-22154600	Weak transcription	Fetal Brain Male	brain
43	chr22:22139800-22145600	Strong transcription	K562	blood
44	chr22:22139800-22150600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr22:22139800-22151200	Weak transcription	Pancreas	Pancrea
46	chr22:22140000-22150400	Weak transcription	Lung	lung
47	chr22:22140200-22147400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr22:22140800-22161800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr22:22141000-22145600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr22:22141000-22145600	Strong transcription	Muscle Satellite Cultured Cells	--

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