Variant report

Variant	rs6006242
Chromosome Location	chr22:30166630-30166631
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:30165385-30167411	K562	blood:	n/a	n/a
2	POLR2A	chr22:30166393-30167739	HepG2	liver:	n/a	n/a
3	MAFK	chr22:30166509-30166633	HepG2	liver:	n/a	n/a
4	POLR2A	chr22:30166471-30167199	K562	blood:	n/a	n/a
5	POLR2A	chr22:30165993-30167302	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr22:30166461-30166726	HepG2	liver:	n/a	n/a
7	POLR2A	chr22:30166395-30166708	K562	blood:	n/a	n/a
8	POLR2A	chr22:30166340-30166686	GM12878	blood:	n/a	n/a
9	POLR2A	chr22:30166360-30166986	K562	blood:	n/a	n/a
10	POLR2A	chr22:30165599-30167109	K562	blood:	n/a	n/a
11	POLR2A	chr22:30165652-30167082	HepG2	liver:	n/a	n/a
12	POLR2A	chr22:30166392-30166758	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30165546..30168026-chr22:30174999..30177192,2	MCF-7	breast:
2	chr22:30145045..30147687-chr22:30166151..30168873,2	MCF-7	breast:
3	chr22:30165843..30167692-chr22:30176073..30180493,3	MCF-7	breast:
4	chr22:30160959..30163738-chr22:30164422..30168687,4	MCF-7	breast:
5	chr22:30117740..30119771-chr22:30165612..30167453,2	MCF-7	breast:

No data

Variant related genes	Relation type
ZMAT5	TF binding region
ENSG00000184076	Chromatin interaction
ENSG00000100319	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1071962	1.00[JPT][hapmap]
rs12158466	1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12159277	1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12627866	1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12628028	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12628234	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12628545	1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs14115	1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16987142	1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16988049	1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17711461	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17711508	1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2018808	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2240364	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2240365	1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2240366	1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249399	0.81[ASN][1000 genomes]
rs249402	0.81[ASN][1000 genomes]
rs28730892	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57122143	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58015017	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs5997518	0.88[EUR][1000 genomes]
rs5997519	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5997520	1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5997524	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6006241	0.88[EUR][1000 genomes]
rs6006247	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6006249	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6006250	1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6006262	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60805530	0.83[EUR][1000 genomes]
rs61616383	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7285660	1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7285800	1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7287777	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs73392899	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73394814	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73394831	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73394838	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs737721	0.92[ASN][1000 genomes]
rs737728	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs740116	1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8138165	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv817987	chr22:30163526-30169436	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30164400-30167400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr22:30164600-30171000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr22:30164600-30183800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr22:30164600-30185000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr22:30164600-30188600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr22:30164800-30167000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr22:30164800-30167200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr22:30164800-30167400	Strong transcription	Fetal Thymus	thymus
9	chr22:30164800-30167600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr22:30165000-30166800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
11	chr22:30165000-30167000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr22:30165000-30167200	Strong transcription	A549	lung
13	chr22:30165000-30167400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr22:30165000-30167400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr22:30165000-30167400	Strong transcription	Osteobl	bone
16	chr22:30165000-30172400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr22:30165200-30166800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr22:30165200-30166800	Strong transcription	Primary T cells from cord blood	blood
19	chr22:30165200-30166800	Strong transcription	Pancreas	Pancrea
20	chr22:30165200-30166800	Strong transcription	NH-A	brain
21	chr22:30165200-30167000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr22:30165200-30167000	Strong transcription	Fetal Brain Female	brain
23	chr22:30165200-30167000	Strong transcription	NHEK	skin
24	chr22:30165200-30167200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr22:30165200-30167400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr22:30165200-30167400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr22:30165200-30167400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr22:30165200-30167400	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr22:30165200-30167800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr22:30165200-30168400	Weak transcription	NHDF-Ad	bronchial
31	chr22:30165200-30168800	Strong transcription	Fetal Stomach	stomach
32	chr22:30165400-30166800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr22:30165400-30166800	Strong transcription	Primary hematopoietic stem cells	blood
34	chr22:30165400-30166800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr22:30165400-30166800	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr22:30165400-30166800	Strong transcription	Colon Smooth Muscle	Colon
37	chr22:30165400-30166800	Strong transcription	K562	blood
38	chr22:30165400-30167000	Strong transcription	Adipose Nuclei	Adipose
39	chr22:30165400-30167000	Strong transcription	Brain Angular Gyrus	brain
40	chr22:30165400-30167000	Strong transcription	Brain Germinal Matrix	brain
41	chr22:30165400-30167000	Strong transcription	Dnd41	blood
42	chr22:30165400-30167000	Strong transcription	HSMM	muscle
43	chr22:30165400-30167200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr22:30165400-30167200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr22:30165400-30167200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr22:30165400-30167200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr22:30165400-30167200	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr22:30165400-30167200	Strong transcription	Brain Hippocampus Middle	brain
49	chr22:30165400-30167200	Strong transcription	Lung	lung
50	chr22:30165400-30167200	Strong transcription	Ovary	ovary

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