Variant report

Variant	rs72706084
Chromosome Location	chr1:169453703-169453704
allele	C/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	CCNT2	chr1:169452763-169453712	K562	blood:	n/a	n/a
2	POLR2A	chr1:169452374-169456758	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr1:169452668-169456351	Hela-S3	cervix:	n/a	n/a
4	STAT3	chr1:169453358-169453726	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr1:169452665-169453713	HepG2	liver:	n/a	n/a
6	CHD2	chr1:169453025-169453724	K562	blood:	n/a	n/a
7	MYC	chr1:169452634-169454733	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr1:169452844-169453743	MCF10A-Er-Src	breast:	n/a	chr1:169452868-169452880
9	SIN3AK20	chr1:169452581-169456049	MCF-7	breast:	n/a	n/a
10	JUND	chr1:169452750-169453715	K562	blood:	n/a	chr1:169452868-169452880
11	POLR2A	chr1:169451934-169453706	K562	blood:	n/a	n/a
12	POLR2A	chr1:169452556-169453875	H1-hESC	embryonic stem cell:	n/a	n/a
13	FOS	chr1:169453298-169453741	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr1:169453309-169453726	MCF10A-Er-Src	breast:	n/a	n/a
15	E2F4	chr1:169452857-169453848	MCF10A-Er-Src	breast:	n/a	chr1:169453020-169453027
16	STAT3	chr1:169452857-169453801	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr1:169452526-169456603	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr1:169451926-169456727	IMR90	lung:	n/a	n/a
19	HCFC1	chr1:169452490-169456441	Hela-S3	cervix:	n/a	n/a
20	STAT3	chr1:169452866-169453779	MCF10A-Er-Src	breast:	n/a	n/a
21	CHD1	chr1:169452645-169456936	IMR90	lung:	n/a	chr1:169453020-169453027 chr1:169455009-169455019 chr1:169454476-169454486
22	MYC	chr1:169452753-169453780	MCF10A-Er-Src	breast:	n/a	n/a
23	MXI1	chr1:169452580-169456608	IMR90	lung:	n/a	n/a
24	RCOR1	chr1:169452731-169453709	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:169451858..169456935-chr1:169476541..169486862,15	MCF-7	breast:
2	chr1:169337822..169339719-chr1:169451874..169454199,3	K562	blood:
3	chr1:169449894..169459462-chr1:169475885..169501963,75	MCF-7	breast:
4	chr1:169338121..169342264-chr1:169451874..169455112,4	K562	blood:
5	chr1:169452217..169454597-chr1:169772651..169775174,2	K562	blood:
6	chr1:169434019..169436756-chr1:169452207..169454585,3	MCF-7	breast:
7	chr1:169325315..169327435-chr1:169453346..169454920,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213062	TF binding region
ENSG00000198734	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10489190	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10494477	1.00[AFR][1000 genomes]
rs10494478	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10800433	1.00[AFR][1000 genomes]
rs10919122	1.00[AFR][1000 genomes]
rs10919123	1.00[AFR][1000 genomes]
rs10919125	1.00[AFR][1000 genomes]
rs10919127	1.00[AFR][1000 genomes]
rs10919147	1.00[AFR][1000 genomes]
rs10919149	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10919150	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10919153	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10919158	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10919162	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10919165	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10919172	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12022617	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12022768	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12025397	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12025721	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12028208	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12029800	1.00[AFR][1000 genomes]
rs12030541	1.00[AFR][1000 genomes]
rs12030810	1.00[AFR][1000 genomes]
rs12031371	1.00[AFR][1000 genomes]
rs12036426	1.00[AFR][1000 genomes]
rs12037926	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12042990	1.00[AFR][1000 genomes]
rs12044982	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12045803	1.00[AFR][1000 genomes]
rs12401962	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12402774	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12405185	1.00[AFR][1000 genomes]
rs12405725	1.00[AFR][1000 genomes]
rs12567342	1.00[AFR][1000 genomes]
rs1517742	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1517746	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17345426	1.00[AFR][1000 genomes]
rs17345531	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs17349677	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs17518147	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17576927	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1949426	0.86[ASN][1000 genomes]
rs2092083	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766100	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3766101	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4497270	1.00[AFR][1000 genomes]
rs4562680	1.00[AFR][1000 genomes]
rs72704035	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7414819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522565	0.93[ASN][1000 genomes]
rs7546361	0.93[ASN][1000 genomes]
rs7554853	0.86[ASN][1000 genomes]
rs7556463	1.00[AFR][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	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers 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 target site	28 gene(s)	inside rSNPs	diseases
3	nsv1001454	chr1:169387381-169465274	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1005941	chr1:169410486-169456393	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 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	chr1:169430000-169453800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:169430000-169454000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:169430000-169454400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:169430000-169454400	Weak transcription	Spleen	Spleen
5	chr1:169444200-169454000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:169446800-169454200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:169446800-169454200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:169448000-169457000	Active TSS	Right Ventricle	heart
9	chr1:169450000-169456000	Active TSS	Psoas Muscle	Psoas
10	chr1:169451000-169453800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:169451000-169454000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:169451600-169457000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:169451800-169453800	Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr1:169451800-169455400	Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr1:169452000-169453800	Enhancers	Primary hematopoietic stem cells	blood
16	chr1:169452000-169453800	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr1:169452000-169454200	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr1:169452200-169453800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr1:169452200-169456200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:169452400-169454200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr1:169452400-169454200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr1:169452400-169454200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr1:169452400-169454400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:169452400-169454800	Active TSS	Right Atrium	heart
25	chr1:169452600-169453800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr1:169452600-169453800	Enhancers	Fetal Muscle Leg	muscle
27	chr1:169452600-169453800	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr1:169452600-169453800	Flanking Active TSS	HSMM	muscle
29	chr1:169452600-169454000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr1:169452600-169454000	Flanking Active TSS	Brain Anterior Caudate	brain
31	chr1:169452600-169454000	Enhancers	HUVEC	blood vessel
32	chr1:169452600-169454200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:169452600-169454200	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr1:169452600-169454200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:169452600-169454200	Flanking Active TSS	Hela-S3	cervix
36	chr1:169452600-169454400	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr1:169452600-169454400	Flanking Active TSS	Fetal Intestine Small	intestine
38	chr1:169452600-169454600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:169452600-169454600	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr1:169452600-169454600	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr1:169452600-169454800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:169452600-169455600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:169452600-169457000	Active TSS	Left Ventricle	heart
44	chr1:169452800-169453800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr1:169452800-169453800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:169452800-169453800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr1:169452800-169453800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr1:169452800-169454000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr1:169452800-169454000	Flanking Active TSS	Fetal Brain Male	brain
50	chr1:169452800-169454000	Active TSS	Fetal Kidney	kidney

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