Variant report

Variant	rs5749998
Chromosome Location	chr22:22162374-22162375
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:22160454..22162385-chr22:22220986..22222936,2	MCF-7	breast:
2	chr22:22137496..22139412-chr22:22161128..22163592,2	K562	blood:
3	chr22:22139546..22142407-chr22:22162132..22163873,3	K562	blood:
4	chr22:22162010..22163594-chr22:22257433..22259936,2	K562	blood:
5	chr22:22125720..22128636-chr22:22161159..22162923,2	K562	blood:
6	chr22:22162194..22165063-chr22:22219763..22221740,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100030	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11704205	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13943	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1892846	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1892848	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2006893	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2266967	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283792	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2283794	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2298432	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs240049	0.89[CEU][hapmap]
rs28566555	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34550586	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3788332	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3810609	0.85[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3810610	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4478016	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4516540	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4821402	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55762115	0.80[EUR][1000 genomes]
rs5749806	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5749937	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5749986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5750113	0.96[CEU][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5755099	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5755654	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5755694	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5999515	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]
rs5999521	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5999550	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]
rs5999750	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6518986	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6928	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs743409	1.00[CEU][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes]
rs8136590	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8136867	0.82[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8141851	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9607287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9607340	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9607347	0.87[EUR][1000 genomes]
rs9610315	0.87[AFR][1000 genomes]
rs9610371	0.82[AFR][1000 genomes]
rs9610375	0.96[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9610400	0.90[AFR][1000 genomes]
rs9610458	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9610500	0.81[ASN][1000 genomes]
rs9610505	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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
20	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
21	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
22	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
23	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs5749998	LL22NC03-86G7.1	cis	Adipose Subcutaneous	GTEx
rs5749998	LL22NC03-86G7.1	cis	Nerve Tibial	GTEx
rs5749998	PPM1F	cis	uninvolved skin	skin_eQTL
rs5749998	TOP3BP1	cis	Adipose Subcutaneous	GTEx
rs5749998	LL22NC03-86G7.1	cis	Heart Left Ventricle	GTEx
rs5749998	LL22NC03-86G7.1	cis	Whole Blood	GTEx
rs5749998	LL22NC03-86G7.1	cis	Thyroid	GTEx
rs5749998	MAPK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 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	chr22:22127200-22167600	Weak transcription	Psoas Muscle	Psoas
5	chr22:22127200-22170600	Weak transcription	Hela-S3	cervix
6	chr22:22135800-22162400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr22:22135800-22162600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr22:22135800-22162600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr22:22136000-22162400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr22:22137600-22162600	Strong transcription	Dnd41	blood
11	chr22:22139200-22172800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr22:22142800-22170600	Weak transcription	Colonic Mucosa	Colon
13	chr22:22145800-22170600	Weak transcription	Small Intestine	intestine
14	chr22:22147600-22162800	Strong transcription	K562	blood
15	chr22:22149600-22162600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr22:22149800-22162400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr22:22150600-22162400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr22:22150600-22162400	Strong transcription	Primary B cells from cord blood	blood
19	chr22:22150800-22162600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr22:22151200-22162400	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr22:22151800-22162400	Strong transcription	GM12878-XiMat	blood
22	chr22:22152600-22162600	Strong transcription	Adipose Nuclei	Adipose
23	chr22:22156600-22162600	Weak transcription	Fetal Brain Male	brain
24	chr22:22157000-22162600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr22:22160000-22164800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr22:22160000-22167600	Weak transcription	Pancreas	Pancrea
27	chr22:22160000-22171600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr22:22160200-22164800	Weak transcription	Fetal Intestine Small	intestine
29	chr22:22160400-22171200	Weak transcription	Right Ventricle	heart
30	chr22:22160600-22171800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr22:22160600-22172800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr22:22160800-22163000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr22:22160800-22171400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr22:22160800-22171400	Weak transcription	Gastric	stomach
35	chr22:22160800-22172400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr22:22161000-22169800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr22:22161000-22170400	Weak transcription	HMEC	breast
38	chr22:22161000-22171400	Weak transcription	Esophagus	oesophagus
39	chr22:22161200-22162600	Enhancers	Brain Anterior Caudate	brain
40	chr22:22161200-22162600	Enhancers	Rectal Smooth Muscle	rectum
41	chr22:22161200-22166200	Weak transcription	Fetal Brain Female	brain
42	chr22:22161200-22167800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr22:22161400-22162400	Genic enhancers	Fetal Muscle Leg	muscle
44	chr22:22161400-22162600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr22:22161400-22162600	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr22:22161400-22163400	Enhancers	Colon Smooth Muscle	Colon
47	chr22:22161400-22169800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr22:22161400-22173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr22:22161600-22162400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr22:22161600-22162400	Enhancers	Stomach Smooth Muscle	stomach

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