Variant report

Variant	rs4354572
Chromosome Location	chr1:173444836-173444837
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr1:173444797-173445874	MCF10A-Er-Src	breast:	n/a	chr1:173445057-173445067 chr1:173445057-173445067
2	POLR2A	chr1:173444833-173445208	SK-N-SH	brain:	n/a	n/a
3	E2F4	chr1:173444740-173445160	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr1:173444795-173445297	MCF10A-Er-Src	breast:	n/a	chr1:173445057-173445067 chr1:173445057-173445067
5	MXI1	chr1:173444253-173448100	IMR90	lung:	n/a	chr1:173447831-173447846
6	MYC	chr1:173444793-173445230	MCF10A-Er-Src	breast:	n/a	n/a
7	KAP1	chr1:173444758-173446206	HEK293	kidney:	n/a	n/a
8	HEY1	chr1:173444814-173445154	HepG2	liver:	n/a	n/a
9	FOXA1	chr1:173444735-173445230	HepG2	liver:	n/a	n/a
10	JUN	chr1:173444105-173448462	K562	blood:	n/a	chr1:173446953-173446961 chr1:173445057-173445067 chr1:173447039-173447048 chr1:173445057-173445067
11	HCFC1	chr1:173444740-173448059	Hela-S3	cervix:	n/a	n/a
12	CEBPB	chr1:173444811-173445362	Hela-S3	cervix:	n/a	n/a
13	MAX	chr1:173444772-173445472	SK-N-SH	brain:	n/a	n/a
14	MXI1	chr1:173444135-173448173	SK-N-SH	brain:	n/a	chr1:173447831-173447846
15	STAT3	chr1:173444825-173445171	MCF10A-Er-Src	breast:	n/a	n/a
16	MAZ	chr1:173444567-173447830	IMR90	lung:	n/a	n/a
17	FOSL2	chr1:173444832-173445370	SK-N-SH	brain:	n/a	chr1:173445057-173445067 chr1:173445057-173445067
18	POLR2A	chr1:173444798-173445207	MCF10A-Er-Src	breast:	n/a	n/a
19	STAT3	chr1:173444799-173445160	MCF10A-Er-Src	breast:	n/a	n/a
20	STAT3	chr1:173444805-173445240	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:173444743..173447866-chr1:173792301..173795321,5	MCF-7	breast:
2	chr1:173442552..173449186-chr1:173835087..173838637,8	MCF-7	breast:
3	chr1:173444678..173448018-chr1:173835571..173838629,5	K562	blood:
4	chr1:173442536..173447801-chr1:173833439..173838851,7	K562	blood:
5	chr1:173443316..173450639-chr1:173791413..173797919,15	K562	blood:
6	chr1:173443428..173450639-chr1:173791407..173797248,10	K562	blood:

Variant related genes	Relation type
PRDX6	TF binding region
ENSG00000117593	Chromatin interaction
ENSG00000208317	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000120334	Chromatin interaction
ENSG00000185278	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10157668	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs10158034	1.00[GIH][hapmap]
rs10732994	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10737302	1.00[ASW][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12059068	1.00[GIH][hapmap]
rs12065033	1.00[GIH][hapmap]
rs12081220	1.00[GIH][hapmap]
rs12087885	1.00[GIH][hapmap]
rs16828416	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs16846025	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs16846029	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs16846052	1.00[GIH][hapmap]
rs16846055	0.81[YRI][hapmap];1.00[AMR][1000 genomes]
rs16846090	1.00[AMR][1000 genomes]
rs16846099	1.00[AMR][1000 genomes]
rs16846103	1.00[AMR][1000 genomes]
rs16846122	1.00[AMR][1000 genomes]
rs16846125	1.00[AMR][1000 genomes]
rs16846129	1.00[AMR][1000 genomes]
rs16846173	0.87[ASW][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs16846204	1.00[AMR][1000 genomes]
rs16846220	1.00[GIH][hapmap]
rs16846301	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs2013387	1.00[GIH][hapmap]
rs35581908	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4342885	0.93[ASW][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4494170	1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap]
rs4551627	0.92[AFR][1000 genomes]
rs4567310	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4636504	0.82[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4916221	1.00[GIH][hapmap]
rs56043618	1.00[AMR][1000 genomes]
rs56236728	0.87[AMR][1000 genomes]
rs59041016	1.00[AMR][1000 genomes]
rs60055251	0.87[AMR][1000 genomes]
rs60769229	0.87[AMR][1000 genomes]
rs6663036	0.87[AMR][1000 genomes]
rs6678784	1.00[GIH][hapmap]
rs7513591	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7513763	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425410	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425722	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9425725	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9425727	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831915	chr1:173268424-173482157	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173430800-173445000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr1:173438200-173445000	Weak transcription	Primary B cells from cord blood	blood
3	chr1:173440400-173445200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:173440600-173445200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:173440600-173445200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:173440600-173445800	Weak transcription	Spleen	Spleen
7	chr1:173441000-173445000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:173441200-173445000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:173441200-173445000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:173441400-173445200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr1:173441600-173445200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:173442400-173445000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:173442400-173445200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr1:173442400-173445200	Enhancers	Fetal Intestine Large	intestine
15	chr1:173442400-173445200	Enhancers	Fetal Intestine Small	intestine
16	chr1:173442400-173445200	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr1:173442600-173445000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:173442800-173445000	Enhancers	Primary T cells fromperipheralblood	blood
19	chr1:173443200-173445000	Weak transcription	Gastric	stomach
20	chr1:173443200-173445200	Weak transcription	Ovary	ovary
21	chr1:173443600-173445000	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr1:173443600-173445200	Enhancers	Placenta Amnion	Placenta Amnion
23	chr1:173443600-173445200	Active TSS	HepG2	liver
24	chr1:173443600-173445800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr1:173443600-173447400	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr1:173443600-173447800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:173443800-173445200	Weak transcription	Aorta	Aorta
28	chr1:173443800-173445200	Enhancers	Esophagus	oesophagus
29	chr1:173443800-173445400	Weak transcription	Fetal Kidney	kidney
30	chr1:173443800-173447600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:173444000-173445000	Weak transcription	Pancreas	Pancrea
32	chr1:173444000-173445400	Flanking Active TSS	Stomach Smooth Muscle	stomach
33	chr1:173444000-173448000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr1:173444200-173445000	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr1:173444200-173445000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:173444200-173445000	Enhancers	Colonic Mucosa	Colon
37	chr1:173444200-173445200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:173444200-173445200	Enhancers	Small Intestine	intestine
39	chr1:173444200-173445400	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr1:173444200-173445600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:173444200-173445600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr1:173444200-173445800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr1:173444200-173445800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:173444200-173446000	Flanking Active TSS	Liver	Liver
45	chr1:173444200-173447400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:173444200-173447400	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr1:173444400-173445000	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr1:173444400-173445000	Active TSS	Rectal Smooth Muscle	rectum
49	chr1:173444400-173445000	Weak transcription	Right Atrium	heart
50	chr1:173444400-173445000	Active TSS	Thymus	Thymus

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