Variant report

Variant	rs4953848
Chromosome Location	chr2:110373849-110373850
allele	A/G
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	POLR2A	chr2:110373655-110374649	IMR90	lung:	n/a	n/a
2	POLR2A	chr2:110373728-110373974	Hela-S3	cervix:	n/a	n/a
3	MYBL2	chr2:110370502-110374022	HepG2	liver:	n/a	chr2:110371047-110371062
4	POLR2A	chr2:110373772-110373933	ProgFib	skin:	n/a	n/a
5	ARID3A	chr2:110373405-110373978	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:110369085-110379088	Hela-S3	cervix:	n/a	n/a
7	HNF4G	chr2:110373303-110373917	HepG2	liver:	n/a	chr2:110373615-110373630
8	RCOR1	chr2:110370666-110373874	Hela-S3	cervix:	n/a	n/a
9	MAX	chr2:110370986-110373857	HepG2	liver:	n/a	n/a
10	POLR2A	chr2:110370305-110374042	Hela-S3	cervix:	n/a	n/a
11	STAT3	chr2:110373679-110373970	MCF10A-Er-Src	breast:	n/a	chr2:110373796-110373807
12	E2F4	chr2:110373809-110374009	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr2:110370315-110373849	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr2:110372608-110374359	Hela-S3	cervix:	n/a	n/a
15	SMARCB1	chr2:110370815-110373912	Hela-S3	cervix:	n/a	n/a
16	CREB1	chr2:110370897-110374076	HepG2	liver:	n/a	n/a
17	MBD4	chr2:110373277-110374037	HepG2	liver:	n/a	n/a
18	ZNF263	chr2:110370375-110374014	HEK293-T-REx	kidney:	n/a	n/a
19	SIN3A	chr2:110370556-110373917	H1-hESC	embryonic stem cell:	n/a	chr2:110371213-110371224 chr2:110370971-110370982
20	STAT3	chr2:110373606-110373933	MCF10A-Er-Src	breast:	n/a	chr2:110373796-110373807
21	CHD2	chr2:110372804-110373938	Hela-S3	cervix:	n/a	n/a
22	MXI1	chr2:110370718-110373948	HepG2	liver:	n/a	n/a
23	MXI1	chr2:110372606-110373913	Hela-S3	cervix:	n/a	n/a
24	STAT3	chr2:110373801-110374134	MCF10A-Er-Src	breast:	n/a	n/a
25	MAX	chr2:110370845-110374026	HepG2	liver:	n/a	n/a
26	HNF4A	chr2:110373320-110373883	HepG2	liver:	n/a	chr2:110373616-110373631
27	POLR2A	chr2:110372644-110373958	HepG2	liver:	n/a	n/a
28	CHD1	chr2:110369172-110374773	IMR90	lung:	n/a	n/a
29	MBD4	chr2:110372752-110374121	HepG2	liver:	n/a	n/a
30	POLR2A	chr2:110373203-110374178	HepG2	liver:	n/a	n/a
31	GTF2F1	chr2:110372921-110373961	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr2:110369290-110378742	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr2:110373243-110373910	HepG2	liver:	n/a	n/a
34	RCOR1	chr2:110372461-110373925	HepG2	liver:	n/a	n/a
35	WRNIP1	chr2:110373709-110373912	GM12878	blood:	n/a	n/a
36	HEY1	chr2:110370629-110374055	HepG2	liver:	n/a	chr2:110371173-110371188 chr2:110371184-110371199 chr2:110371221-110371236
37	HNF4G	chr2:110373353-110373881	HepG2	liver:	n/a	chr2:110373615-110373630
38	MYBL2	chr2:110373300-110373959	HepG2	liver:	n/a	n/a
39	USF2	chr2:110372958-110373933	Hela-S3	cervix:	n/a	n/a
40	MAZ	chr2:110370997-110374016	HepG2	liver:	n/a	n/a
41	MAX	chr2:110370814-110374043	HepG2	liver:	n/a	n/a
42	MAX	chr2:110370659-110373951	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr2:110372595-110374150	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:110373614..110376215-chr2:110402569..110405240,2	MCF-7	breast:
2	chr2:110365749..110368166-chr2:110372173..110374120,2	MCF-7	breast:
3	chr2:110373452..110379192-chr2:110379492..110383330,5	MCF-7	breast:
4	chr2:110372868..110375029-chr2:110390874..110393546,2	MCF-7	breast:

Variant related genes	Relation type
SEPT10	TF binding region

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

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

rs_ID	r²[population]
rs1036317	0.84[EUR][1000 genomes]
rs1036318	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10496432	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1811388	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28441405	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28445980	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28570680	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28612440	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28696274	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28719680	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3213866	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs34111852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34311530	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs34441132	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34517320	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs34821058	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35120088	0.83[AMR][1000 genomes]
rs35223862	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35392016	0.83[AMR][1000 genomes]
rs35550721	0.85[EUR][1000 genomes]
rs35955221	0.83[AMR][1000 genomes]
rs4482487	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4953729	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4953730	0.81[AFR][1000 genomes]
rs4953788	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4953847	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953853	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55794045	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs56265736	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56794190	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs58031484	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6594050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6594053	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6594054	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6709945	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6719215	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6725792	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6737736	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751785	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6760577	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72824788	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72824796	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72824802	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72826816	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72826817	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs753492	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7565483	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7577865	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs892462	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9330317	0.83[AMR][1000 genomes]
rs9330321	0.83[AMR][1000 genomes]
rs9752531	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9798179	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874777	chr2:109825516-110693317	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874780	chr2:110078080-110432886	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1011456	chr2:110290958-110980402	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv535861	chr2:110290958-110980402	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats 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	60 gene(s)	inside rSNPs	diseases
5	nsv482469	chr2:110302488-110452580	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1009367	chr2:110349178-110863354	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv829617	chr2:110359857-110380012	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	esv2762780	chr2:110367969-110462496	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110369400-110374600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:110369600-110374000	Active TSS	Hela-S3	cervix
3	chr2:110369800-110374200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:110370000-110374000	Active TSS	Fetal Kidney	kidney
5	chr2:110370000-110374800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:110370000-110375000	Active TSS	NHEK	skin
7	chr2:110372600-110374000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
8	chr2:110372600-110374000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr2:110372600-110374000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:110372600-110374000	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr2:110372600-110374000	Flanking Active TSS	NH-A	brain
12	chr2:110372600-110374200	Flanking Active TSS	Fetal Brain Female	brain
13	chr2:110372600-110374200	Flanking Active TSS	HUVEC	blood vessel
14	chr2:110372600-110374800	Enhancers	Fetal Heart	heart
15	chr2:110372800-110374000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
16	chr2:110372800-110374000	Bivalent/Poised TSS	Fetal Thymus	thymus
17	chr2:110372800-110374000	Flanking Active TSS	Osteobl	bone
18	chr2:110372800-110374200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr2:110372800-110374200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:110373000-110374000	Flanking Active TSS	Fetal Lung	lung
21	chr2:110373000-110374200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:110373000-110374200	Flanking Active TSS	Rectal Smooth Muscle	rectum
23	chr2:110373000-110375800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:110373200-110374000	Enhancers	Gastric	stomach
25	chr2:110373200-110374200	Flanking Active TSS	Fetal Intestine Large	intestine
26	chr2:110373200-110374600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:110373200-110374600	Enhancers	Muscle Satellite Cultured Cells	--
28	chr2:110373200-110375400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:110373400-110374000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:110373400-110374000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr2:110373400-110374000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
32	chr2:110373400-110374000	Flanking Active TSS	Fetal Muscle Leg	muscle
33	chr2:110373400-110374000	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr2:110373400-110374000	Bivalent/Poised TSS	HepG2	liver
35	chr2:110373400-110374000	Active TSS	NHLF	lung
36	chr2:110373400-110374200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
37	chr2:110373400-110374200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:110373400-110374200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:110373400-110374200	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr2:110373400-110374200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr2:110373400-110374400	Flanking Active TSS	A549	lung
42	chr2:110373400-110374600	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr2:110373400-110374800	Flanking Active TSS	Brain Germinal Matrix	brain
44	chr2:110373600-110374000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:110373600-110374000	Active TSS	Colonic Mucosa	Colon
46	chr2:110373600-110374000	Active TSS	Esophagus	oesophagus
47	chr2:110373600-110374000	Flanking Active TSS	Fetal Brain Male	brain
48	chr2:110373600-110374000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr2:110373600-110374000	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr2:110373600-110374200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell

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