Variant report

Variant	rs7550170
Chromosome Location	chr1:45225574-45225575
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45224410-45227043	K562	blood:	n/a	n/a
2	POLR2A	chr1:45225325-45226722	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr1:45224566-45227109	K562	blood:	n/a	n/a
4	POLR2A	chr1:45224569-45225851	HL-60	blood:	n/a	n/a
5	POLR2A	chr1:45224405-45227009	K562	blood:	n/a	n/a
6	POLR2A	chr1:45224555-45226798	K562	blood:	n/a	n/a
7	POLR2A	chr1:45224471-45227096	K562	blood:	n/a	n/a
8	POLR2A	chr1:45225336-45226159	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr1:45224561-45227047	K562	blood:	n/a	n/a
10	POLR2A	chr1:45225412-45226500	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:45225315-45225996	HepG2	liver:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45224240..45226290-chr1:45308445..45310205,2	K562	blood:
2	chr1:45223594..45225886-chr1:45284198..45286791,2	K562	blood:
3	chr1:45171946..45173521-chr1:45223386..45225623,2	MCF-7	breast:

No data

Variant related genes	Relation type
KIF2C	TF binding region
ENSG00000202444	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000226499	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10127448	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10465818	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11211030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11211031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11211034	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11584031	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs11801067	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11808189	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11808852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12059964	0.88[CEU][hapmap];0.86[YRI][hapmap]
rs12094028	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12117881	0.83[ASN][1000 genomes]
rs12136048	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136099	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12410588	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12732939	0.84[YRI][hapmap]
rs12742914	0.90[ASN][1000 genomes]
rs12746270	0.83[YRI][hapmap]
rs16832228	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs263986	0.81[JPT][hapmap]
rs3820586	0.83[YRI][hapmap]
rs4542248	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6429548	0.96[CEU][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6656337	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6658470	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666987	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671255	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6678729	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685176	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6688710	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689911	0.83[YRI][hapmap]
rs6698847	0.81[AMR][1000 genomes]
rs7512710	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7518836	0.93[ASN][1000 genomes]
rs7524446	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs7525308	0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap]
rs7534487	0.84[YRI][hapmap]
rs7536146	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7555065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9988580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
3	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
4	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
5	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
6	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
7	nsv998871	chr1:45196587-45251179	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	171 gene(s)	inside rSNPs	diseases
8	nsv461406	chr1:45218542-45293518	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
9	nsv546145	chr1:45218542-45293518	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45205800-45240600	Weak transcription	Ovary	ovary
2	chr1:45206000-45240400	Weak transcription	Right Atrium	heart
3	chr1:45206200-45225800	Weak transcription	Primary T cells from cord blood	blood
4	chr1:45206200-45227400	Weak transcription	Colonic Mucosa	Colon
5	chr1:45206200-45230200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:45206200-45240400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:45206200-45240600	Weak transcription	Stomach Mucosa	stomach
8	chr1:45206400-45232800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:45206400-45240600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:45206600-45240600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:45206800-45226600	Weak transcription	Fetal Brain Male	brain
12	chr1:45206800-45240200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:45207000-45233800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:45207200-45234200	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr1:45207200-45234400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:45207400-45233800	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:45207600-45233800	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:45207600-45234400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:45208600-45233400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:45208600-45234000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:45208800-45234400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:45209400-45235200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:45211200-45233800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:45211400-45229400	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr1:45211400-45233600	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr1:45211400-45234800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:45211400-45235000	Strong transcription	Fetal Stomach	stomach
28	chr1:45211600-45231200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:45211600-45234600	Strong transcription	Fetal Muscle Trunk	muscle
30	chr1:45211600-45235200	Strong transcription	Thymus	Thymus
31	chr1:45211800-45229400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:45211800-45229400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:45212000-45235000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:45212000-45235200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:45212400-45234800	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr1:45212400-45235000	Strong transcription	Fetal Thymus	thymus
37	chr1:45214400-45240400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr1:45215200-45231000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:45215600-45233600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:45215800-45226400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr1:45216600-45226000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:45217800-45229800	Strong transcription	K562	blood
43	chr1:45217800-45233400	Strong transcription	Fetal Intestine Small	intestine
44	chr1:45218000-45229400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr1:45218000-45240600	Weak transcription	Small Intestine	intestine
46	chr1:45218200-45229400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:45218200-45229400	Strong transcription	HSMM	muscle
48	chr1:45218200-45229800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:45218200-45229800	Strong transcription	NHLF	lung
50	chr1:45218200-45230000	Strong transcription	Osteobl	bone

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