Variant report

Variant	rs743409
Chromosome Location	chr22:22129215-22129216
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:22127790..22129989-chr22:22156925..22159029,2	K562	blood:
2	chr22:22129101..22130763-chr22:22220420..22222313,2	K562	blood:
3	chr22:22127086..22129647-chr22:22272153..22274882,2	K562	blood:
4	chr22:22128803..22129714-chr22:22292654..22293508,2	K562	blood:
5	chr22:22128103..22132629-chr22:22289657..22294176,6	K562	blood:
6	chr22:22128885..22129564-chr22:22292386..22293174,2	MCF-7	breast:
7	chr22:22128700..22129747-chr22:22292035..22293557,11	MCF-7	breast:
8	chr22:22066867..22068132-chr22:22128746..22129659,4	K562	blood:

No data

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

Extended variants
information (count: 52 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs11704205	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13943	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1892846	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs1892848	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs2006893	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2266965	0.83[EUR][1000 genomes]
rs2266967	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2283792	0.82[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.84[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2283794	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.87[EUR][1000 genomes]
rs2298432	0.90[JPT][hapmap]
rs240049	0.89[CEU][hapmap]
rs3788332	0.87[EUR][1000 genomes]
rs3810609	0.90[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3810610	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4478016	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4516540	0.89[EUR][1000 genomes]
rs4821402	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs5749806	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5749937	0.83[EUR][1000 genomes]
rs5749986	0.87[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5749998	1.00[CEU][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes]
rs5750113	0.93[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.87[EUR][1000 genomes]
rs5754941	0.82[ASN][1000 genomes]
rs5755099	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5999515	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]
rs5999521	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5999550	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]
rs5999750	0.83[EUR][1000 genomes]
rs6518986	0.88[EUR][1000 genomes]
rs6928	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8136590	0.88[EUR][1000 genomes]
rs8136867	0.93[ASW][hapmap];0.82[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs8141851	0.91[EUR][1000 genomes]
rs9607287	1.00[CEU][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes]
rs9607347	0.81[EUR][1000 genomes]
rs9610375	0.96[CEU][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823866	chr22:21928916-22131125	Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers 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 miRNA target site	374 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv510804	chr22:22024531-22132764	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	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
11	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
12	nsv1063134	chr22:22067645-22129322	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS 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	18 gene(s)	inside rSNPs	diseases
13	nsv544605	chr22:22067645-22129322	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
14	esv3423141	chr22:22074283-22135439	Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	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
16	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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs743409	MAPK1	Cis_1M	lymphoblastoid	RTeQTL
rs743409	LL22NC03-86G7.1	cis	Muscle Skeletal	GTEx
rs743409	PPM1F	cis	uninvolved skin	skin_eQTL
rs743409	MIF	cis	parietal	SCAN
rs743409	psiTPTE22	cis	parietal	SCAN
rs743409	LL22NC03-86G7.1	cis	Heart Left Ventricle	GTEx
rs743409	DERL3	cis	cerebellum	SCAN
rs743409	LL22NC03-86G7.1	cis	Nerve Tibial	GTEx
rs743409	LL22NC03-86G7.1	cis	Adipose Subcutaneous	GTEx
rs743409	LL22NC03-86G7.1	cis	Whole Blood	GTEx
rs743409	SCARF2	cis	parietal	SCAN
rs743409	LL22NC03-86G7.1	cis	Skin Sun Exposed Lower leg	GTEx
rs743409	LL22NC03-86G7.1	cis	Thyroid	GTEx

Chromatin state (count:126 , 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	chr22:22112400-22136800	Strong transcription	Dnd41	blood
3	chr22:22113400-22163800	Weak transcription	Right Atrium	heart
4	chr22:22113600-22133200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr22:22114200-22172800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr22:22116000-22132800	Strong transcription	K562	blood
7	chr22:22116600-22129400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr22:22117800-22129800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr22:22118800-22133400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr22:22121600-22171400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr22:22122200-22132200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr22:22123200-22133600	Strong transcription	Thymus	Thymus
13	chr22:22123200-22162200	Strong transcription	Fetal Thymus	thymus
14	chr22:22126800-22129400	Strong transcription	Fetal Muscle Leg	muscle
15	chr22:22127000-22130800	Weak transcription	HMEC	breast
16	chr22:22127000-22139200	Weak transcription	Stomach Mucosa	stomach
17	chr22:22127200-22129400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr22:22127200-22129400	Weak transcription	Right Ventricle	heart
19	chr22:22127200-22130400	Weak transcription	Lung	lung
20	chr22:22127200-22130800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr22:22127200-22133000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr22:22127200-22134600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr22:22127200-22136200	Weak transcription	Pancreas	Pancrea
24	chr22:22127200-22138400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr22:22127200-22141000	Weak transcription	Aorta	Aorta
26	chr22:22127200-22142400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr22:22127200-22145200	Weak transcription	Small Intestine	intestine
28	chr22:22127200-22146000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr22:22127200-22167600	Weak transcription	Psoas Muscle	Psoas
30	chr22:22127200-22170600	Weak transcription	Hela-S3	cervix
31	chr22:22127400-22129400	Weak transcription	Fetal Brain Female	brain
32	chr22:22127400-22129600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr22:22127400-22130400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr22:22127400-22130400	Weak transcription	NHLF	lung
35	chr22:22127400-22130600	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr22:22127400-22130600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr22:22127400-22130800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr22:22127400-22130800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr22:22127400-22130800	Weak transcription	Liver	Liver
40	chr22:22127400-22130800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr22:22127400-22130800	Weak transcription	Fetal Lung	lung
42	chr22:22127400-22130800	Weak transcription	Left Ventricle	heart
43	chr22:22127400-22130800	Weak transcription	NHDF-Ad	bronchial
44	chr22:22127400-22131000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr22:22127400-22131000	Weak transcription	Spleen	Spleen
46	chr22:22127400-22131200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr22:22127400-22131200	Weak transcription	Placenta	Placenta
48	chr22:22127400-22131600	Weak transcription	NHEK	skin
49	chr22:22127400-22133000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr22:22127400-22133600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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