Variant report

Variant	rs35957576
Chromosome Location	chr3:111393087-111393088
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	chr3:111393058-111393907	GM12878	blood:	n/a	n/a
2	REST	chr3:111392956-111393676	HL-60	blood:	n/a	chr3:111393097-111393105 chr3:111393505-111393518 chr3:111393424-111393437
3	TBP	chr3:111392902-111393777	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:111392983-111393817	HCT-116	colon:	n/a	n/a
5	POLR2A	chr3:111392979-111393751	ProgFib	skin:	n/a	n/a
6	EP300	chr3:111393004-111393445	GM12878	blood:	n/a	n/a
7	USF1	chr3:111393056-111393699	A549	lung:	n/a	n/a
8	POLR2A	chr3:111393060-111394297	GM19193	blood:	n/a	n/a
9	POLR2A	chr3:111393010-111393834	U87	brain:	n/a	n/a
10	POLR2A	chr3:111392962-111393557	GM12892	blood:	n/a	n/a
11	POLR2A	chr3:111393055-111393750	A549	lung:	n/a	n/a
12	MAX	chr3:111392973-111393785	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr3:111393058-111393830	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr3:111392753-111393720	HCT-116	colon:	n/a	n/a
15	POLR2A	chr3:111392973-111393881	HL-60	blood:	n/a	n/a
16	MAX	chr3:111392779-111394195	A549	lung:	n/a	n/a
17	BHLHE40	chr3:111393023-111393641	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:111393003-111393776	GM12892	blood:	n/a	n/a
19	TAF1	chr3:111393015-111393727	Hela-S3	cervix:	n/a	n/a
20	FOS	chr3:111393080-111393310	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr3:111393081-111393697	U87	brain:	n/a	n/a
22	POLR2A	chr3:111393001-111393702	IMR90	lung:	n/a	n/a
23	MAZ	chr3:111392663-111394399	IMR90	lung:	n/a	n/a
24	MAX	chr3:111392981-111393783	SK-N-SH	brain:	n/a	n/a
25	REST	chr3:111392791-111394991	H1-neurons	neurons:	n/a	chr3:111393097-111393105 chr3:111393505-111393518 chr3:111393424-111393437
26	STAT3	chr3:111393026-111393246	MCF10A-Er-Src	breast:	n/a	chr3:111393141-111393161
27	MXI1	chr3:111392708-111393984	IMR90	lung:	n/a	n/a
28	POLR2A	chr3:111393026-111394044	GM18526	blood:	n/a	n/a
29	NFYB	chr3:111392972-111393728	GM12878	blood:	n/a	chr3:111393438-111393453 chr3:111393464-111393479 chr3:111393435-111393450 chr3:111393464-111393479 chr3:111393438-111393452 chr3:111393440-111393450 chr3:111393464-111393478 chr3:111393464-111393477 chr3:111393438-111393453 chr3:111393463-111393475
30	SMC3	chr3:111392912-111393110	GM12878	blood:	n/a	n/a
31	MAZ	chr3:111392737-111394096	Hela-S3	cervix:	n/a	n/a
32	MAX	chr3:111392941-111393795	ECC-1	luminal epithelium:	n/a	n/a
33	POU2F2	chr3:111393026-111393601	GM12891	blood:	n/a	n/a
34	TCF7L2	chr3:111393004-111393438	PANC-1	pancreas:	n/a	n/a
35	CEBPB	chr3:111392927-111393452	A549	lung:	n/a	n/a
36	SP1	chr3:111392951-111393772	A549	lung:	n/a	chr3:111393510-111393522 chr3:111393439-111393460 chr3:111393510-111393522 chr3:111393403-111393417 chr3:111393511-111393520 chr3:111393465-111393486 chr3:111393512-111393521
37	POLR2A	chr3:111392884-111393879	HL-60	blood:	n/a	n/a
38	CHD1	chr3:111392968-111393314	GM12878	blood:	n/a	n/a
39	POLR2A	chr3:111393045-111394233	GM18505	blood:	n/a	n/a
40	SIN3AK20	chr3:111392879-111393917	HCT-116	colon:	n/a	n/a
41	ZNF263	chr3:111392641-111393696	HEK293-T-REx	kidney:	n/a	chr3:111393375-111393396
42	MAX	chr3:111393035-111393928	MCF-7	breast:	n/a	n/a
43	POLR2A	chr3:111393067-111394132	Hela-S3	cervix:	n/a	n/a
44	PAX5	chr3:111393018-111393709	GM12878	blood:	n/a	n/a
45	TCF12	chr3:111392932-111393926	ECC-1	luminal epithelium:	n/a	chr3:111393517-111393527
46	CHD2	chr3:111393083-111393630	GM12878	blood:	n/a	n/a
47	POLR2A	chr3:111393031-111393809	H1-neurons	neurons:	n/a	n/a
48	RFX5	chr3:111392963-111393870	Hela-S3	cervix:	n/a	chr3:111393441-111393450
49	POLR2A	chr3:111393046-111393782	Raji	blood:	n/a	n/a
50	MTA3	chr3:111392883-111393780	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
PLCXD2	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs13078891	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1355767	0.89[ASN][1000 genomes]
rs1398747	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1606503	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2036995	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2036996	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682052	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4682295	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62275506	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs867293	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111392200-111393200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr3:111392400-111393200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr3:111392400-111393200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:111392400-111393200	Flanking Active TSS	Dnd41	blood
5	chr3:111392400-111393200	Flanking Active TSS	Hela-S3	cervix
6	chr3:111392600-111393200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr3:111392600-111393200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
8	chr3:111392600-111393200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
9	chr3:111392600-111393200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
10	chr3:111392600-111393200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
11	chr3:111392600-111393200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
12	chr3:111392600-111393200	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr3:111392600-111393200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
14	chr3:111392600-111393200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr3:111392600-111393200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:111392600-111393200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr3:111392600-111393200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:111392600-111393200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:111392600-111393200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:111392600-111393200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr3:111392600-111393200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:111392600-111393200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:111392600-111393200	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr3:111392600-111393200	Flanking Active TSS	Liver	Liver
25	chr3:111392600-111393200	Flanking Active TSS	Brain Hippocampus Middle	brain
26	chr3:111392600-111393200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr3:111392600-111393200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
28	chr3:111392600-111393200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr3:111392600-111393200	Flanking Active TSS	GM12878-XiMat	blood
30	chr3:111392600-111393200	Flanking Active TSS	HMEC	breast
31	chr3:111392600-111393200	Flanking Active TSS	NH-A	brain
32	chr3:111392600-111393200	Flanking Active TSS	NHEK	skin
33	chr3:111392600-111393200	Flanking Active TSS	Osteobl	bone
34	chr3:111392600-111393400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr3:111392600-111393600	Active TSS	Stomach Smooth Muscle	stomach
36	chr3:111392600-111393800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr3:111392600-111394000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:111392600-111394000	Active TSS	Brain Substantia Nigra	brain
39	chr3:111392600-111394400	Active TSS	NHDF-Ad	bronchial
40	chr3:111392600-111394400	Active TSS	NHLF	lung
41	chr3:111392600-111395000	Active TSS	Brain Cingulate Gyrus	brain
42	chr3:111392600-111395000	Active TSS	Rectal Smooth Muscle	rectum
43	chr3:111392800-111393200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:111392800-111393200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
45	chr3:111392800-111393200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
46	chr3:111392800-111393200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:111392800-111393200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:111392800-111393200	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr3:111392800-111393200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:111392800-111393200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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