Variant report

Variant	rs5997520
Chromosome Location	chr22:30173177-30173178
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30171892..30174672-chr22:30194273..30195862,2	K562	blood:
2	chr22:30161672..30165971-chr22:30171694..30174809,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100325	Chromatin interaction
ENSG00000100319	Chromatin interaction
ENSG00000184076	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10483156	0.80[CHB][hapmap]
rs1071962	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12158466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12159277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12159536	0.82[EUR][1000 genomes]
rs12163073	0.82[EUR][1000 genomes]
rs12166087	0.80[CHB][hapmap]
rs12627866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12628028	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12628234	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12628545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs14115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16987142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16988011	0.87[YRI][hapmap]
rs16988049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16988062	0.87[YRI][hapmap]
rs17711461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17711508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2018808	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2240364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2240365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2240366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs249399	0.83[ASN][1000 genomes]
rs249402	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs28730892	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57122143	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58015017	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs59394320	0.90[EUR][1000 genomes]
rs5997515	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs5997518	0.90[EUR][1000 genomes]
rs5997519	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5997524	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6006234	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6006235	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6006238	0.82[EUR][1000 genomes]
rs6006239	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6006241	0.90[EUR][1000 genomes]
rs6006242	1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6006247	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6006249	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6006250	1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6006262	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60805530	0.95[EUR][1000 genomes]
rs61616383	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7285660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7285800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7287777	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7289250	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7290420	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs73392899	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73394814	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73394831	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73394838	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs737721	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs737728	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs740116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8138165	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv989381	chr22:30170518-30177035	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv1829662	chr22:30171725-30304390	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30164600-30183800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr22:30164600-30185000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr22:30164600-30188600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr22:30165400-30176800	Weak transcription	Fetal Brain Male	brain
5	chr22:30166000-30176800	Weak transcription	Fetal Kidney	kidney
6	chr22:30166400-30176800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr22:30166600-30176800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr22:30166600-30177000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr22:30166600-30183800	Weak transcription	Aorta	Aorta
10	chr22:30166800-30174200	Weak transcription	Pancreas	Pancrea
11	chr22:30166800-30176400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr22:30166800-30176400	Weak transcription	Colon Smooth Muscle	Colon
13	chr22:30166800-30176400	Weak transcription	Small Intestine	intestine
14	chr22:30166800-30176800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr22:30166800-30176800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr22:30166800-30182800	Weak transcription	Primary T cells from cord blood	blood
17	chr22:30166800-30183000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr22:30166800-30183400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr22:30166800-30183800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr22:30166800-30184200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr22:30166800-30194400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr22:30167000-30174800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr22:30167000-30175000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr22:30167000-30176400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr22:30167000-30176400	Weak transcription	Brain Angular Gyrus	brain
26	chr22:30167000-30176400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr22:30167000-30176600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr22:30167000-30176800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr22:30167000-30176800	Weak transcription	Brain Germinal Matrix	brain
30	chr22:30167000-30180400	Weak transcription	Fetal Brain Female	brain
31	chr22:30167000-30183400	Weak transcription	Primary B cells from cord blood	blood
32	chr22:30167000-30183600	Weak transcription	Dnd41	blood
33	chr22:30167200-30173800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr22:30167200-30174200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr22:30167200-30174800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr22:30167200-30175000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr22:30167200-30175000	Weak transcription	Spleen	Spleen
38	chr22:30167200-30176600	Weak transcription	Brain Hippocampus Middle	brain
39	chr22:30167200-30176600	Weak transcription	Brain Substantia Nigra	brain
40	chr22:30167200-30176600	Weak transcription	Ovary	ovary
41	chr22:30167200-30176800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr22:30167200-30177200	Weak transcription	Lung	lung
43	chr22:30167200-30183000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr22:30167200-30183200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr22:30167200-30183200	Weak transcription	GM12878-XiMat	blood
46	chr22:30167200-30184000	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr22:30167200-30184000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr22:30167200-30187800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr22:30167400-30174000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr22:30167400-30174000	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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