Variant report

Variant	rs9875203
Chromosome Location	chr3:49208480-49208481
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	MAZ	chr3:49208468-49209112	HepG2	liver:	n/a	chr3:49208776-49208783
2	CTCF	chr3:49208293-49208947	GM19240	blood:	n/a	chr3:49208617-49208633 chr3:49208616-49208634 chr3:49208619-49208628 chr3:49208619-49208632 chr3:49208621-49208631
3	CTCF	chr3:49208461-49208755	GM10248	blood:	n/a	chr3:49208617-49208633 chr3:49208616-49208634 chr3:49208619-49208628 chr3:49208619-49208632 chr3:49208621-49208631
4	JUN	chr3:49208074-49209390	K562	blood:	n/a	chr3:49208996-49209005 chr3:49209193-49209202
5	CTCF	chr3:49208444-49208952	GM12892	blood:	n/a	chr3:49208617-49208633 chr3:49208616-49208634 chr3:49208619-49208628 chr3:49208619-49208632 chr3:49208621-49208631
6	CTBP2	chr3:49208354-49209126	H1-hESC	embryonic stem cell:	n/a	n/a
7	YY1	chr3:49208463-49209115	SK-N-SH_RA	brain:	n/a	chr3:49208962-49208973 chr3:49208729-49208743 chr3:49208567-49208581 chr3:49208622-49208636 chr3:49208625-49208639 chr3:49208627-49208636
8	GABPA	chr3:49208434-49208700	K562	blood:	n/a	n/a
9	CTCF	chr3:49208480-49208630	HVMF	connective:	n/a	chr3:49208619-49208628
10	RAD21	chr3:49208399-49209163	IMR90	lung:	n/a	chr3:49208622-49208634 chr3:49208618-49208632 chr3:49208610-49208623 chr3:49208617-49208636 chr3:49208622-49208632 chr3:49208620-49208633
11	POLR2A	chr3:49208478-49209394	HUVEC	blood vessel:	n/a	n/a
12	CTCF	chr3:49208460-49208610	AG04450	lung:	n/a	n/a
13	EBF1	chr3:49208472-49208778	GM12878	blood:	n/a	chr3:49208652-49208663 chr3:49208617-49208628
14	SMC3	chr3:49208414-49208860	Hela-S3	cervix:	n/a	chr3:49208618-49208632 chr3:49208622-49208632
15	MAX	chr3:49208468-49209211	ECC-1	luminal epithelium:	n/a	chr3:49208776-49208783
16	CTCF	chr3:49208131-49209305	SK-N-SH	brain:	n/a	chr3:49208617-49208633 chr3:49208616-49208634 chr3:49208619-49208628 chr3:49208619-49208632 chr3:49208621-49208631
17	GABPA	chr3:49208415-49209188	H1-hESC	embryonic stem cell:	n/a	chr3:49209155-49209164
18	CTCF	chr3:49208435-49208812	A549	lung:	n/a	chr3:49208617-49208633 chr3:49208616-49208634 chr3:49208619-49208628 chr3:49208619-49208632 chr3:49208621-49208631
19	RAD21	chr3:49208438-49208906	ECC-1	luminal epithelium:	n/a	chr3:49208622-49208634 chr3:49208618-49208632 chr3:49208610-49208623 chr3:49208617-49208636 chr3:49208622-49208632 chr3:49208620-49208633
20	RAD21	chr3:49208447-49208749	GM12878	blood:	n/a	chr3:49208622-49208634 chr3:49208618-49208632 chr3:49208610-49208623 chr3:49208617-49208636 chr3:49208622-49208632 chr3:49208620-49208633
21	MAZ	chr3:49208415-49209437	K562	blood:	n/a	chr3:49208776-49208783
22	EBF1	chr3:49208428-49208726	GM12878	blood:	n/a	chr3:49208652-49208663 chr3:49208617-49208628
23	CTCF	chr3:49208444-49208830	H1-hESC	embryonic stem cell:	n/a	chr3:49208617-49208633 chr3:49208616-49208634 chr3:49208619-49208628 chr3:49208619-49208632 chr3:49208621-49208631
24	MAX	chr3:49208421-49209194	ECC-1	luminal epithelium:	n/a	chr3:49208776-49208783
25	ZNF143	chr3:49208428-49208836	GM12878	blood:	n/a	n/a
26	STAT5A	chr3:49208367-49209022	GM12878	blood:	n/a	chr3:49208452-49208461 chr3:49208453-49208462 chr3:49208990-49209002
27	EGR1	chr3:49208436-49208713	K562	blood:	n/a	chr3:49208577-49208587 chr3:49208507-49208516 chr3:49208506-49208519
28	BHLHE40	chr3:49208471-49209212	K562	blood:	n/a	chr3:49208677-49208693 chr3:49208999-49209015
29	POLR2A	chr3:49208369-49209325	H1-neurons	neurons:	n/a	n/a
30	MXI1	chr3:49208067-49212337	SK-N-SH	brain:	n/a	chr3:49211019-49211034 chr3:49211021-49211036
31	SIN3AK20	chr3:49208414-49209184	SK-N-SH	brain:	n/a	n/a
32	RAD21	chr3:49208401-49208817	Hela-S3	cervix:	n/a	chr3:49208622-49208634 chr3:49208618-49208632 chr3:49208610-49208623 chr3:49208617-49208636 chr3:49208622-49208632 chr3:49208620-49208633
33	CTCF	chr3:49208468-49208776	LNCaP	prostate:	n/a	chr3:49208617-49208633 chr3:49208616-49208634 chr3:49208619-49208628 chr3:49208619-49208632 chr3:49208621-49208631
34	POLR2A	chr3:49208344-49209276	H1-neurons	neurons:	n/a	n/a
35	YY1	chr3:49208401-49208826	GM12892	blood:	n/a	chr3:49208729-49208743 chr3:49208567-49208581 chr3:49208622-49208636 chr3:49208625-49208639 chr3:49208627-49208636
36	CTCF	chr3:49208432-49208771	GM13977	blood:	n/a	chr3:49208617-49208633 chr3:49208616-49208634 chr3:49208619-49208628 chr3:49208619-49208632 chr3:49208621-49208631
37	SMC3	chr3:49207950-49209887	SK-N-SH	brain:	n/a	chr3:49208618-49208632 chr3:49208622-49208632
38	POLR2A	chr3:49208410-49209238	HCT-116	colon:	n/a	n/a
39	MAZ	chr3:49208453-49209098	GM12878	blood:	n/a	chr3:49208776-49208783
40	MXI1	chr3:49208466-49208902	GM12878	blood:	n/a	n/a
41	MAZ	chr3:49208447-49208750	Hela-S3	cervix:	n/a	n/a
42	CTCF	chr3:49208234-49209074	HCT-116	colon:	n/a	chr3:49208617-49208633 chr3:49208616-49208634 chr3:49208619-49208628 chr3:49208619-49208632 chr3:49208621-49208631
43	HMGN3	chr3:49208356-49209266	K562	blood:	n/a	n/a
44	ATF2	chr3:49208425-49209055	H1-hESC	embryonic stem cell:	n/a	n/a
45	REST	chr3:49208086-49209551	H1-neurons	neurons:	n/a	chr3:49208982-49208995 chr3:49208985-49208998 chr3:49208898-49208911
46	SMC3	chr3:49208475-49209040	K562	blood:	n/a	chr3:49208618-49208632 chr3:49208622-49208632
47	RAD21	chr3:49208419-49208882	H1-hESC	embryonic stem cell:	n/a	chr3:49208622-49208634 chr3:49208618-49208632 chr3:49208610-49208623 chr3:49208617-49208636 chr3:49208622-49208632 chr3:49208620-49208633
48	TEAD4	chr3:49208414-49209154	K562	blood:	n/a	n/a
49	CTCF	chr3:49208473-49208757	ProgFib	skin:	n/a	chr3:49208617-49208633 chr3:49208616-49208634 chr3:49208619-49208628 chr3:49208619-49208632 chr3:49208621-49208631
50	CTCF	chr3:49208426-49208781	SK-N-SH_RA	brain:	n/a	chr3:49208617-49208633 chr3:49208616-49208634 chr3:49208619-49208628 chr3:49208619-49208632 chr3:49208621-49208631

No.	Distal block	Cell Line	Cell type
1	chr3:49064349..49066955-chr3:49207317..49210098,3	MCF-7	breast:
2	chr3:49208204..49208846-chr3:49486196..49487422,4	K562	blood:
3	chr3:49208330..49210147-chr3:49711158..49712878,2	K562	blood:
4	chr3:49202977..49205406-chr3:49206821..49209199,3	MCF-7	breast:
5	chr3:49202213..49205140-chr3:49207105..49209971,4	MCF-7	breast:
6	chr3:49059138..49060690-chr3:49207989..49210294,2	K562	blood:
7	chr3:49207667..49210496-chr3:49210545..49213014,4	K562	blood:
8	chr3:49207629..49210061-chr3:49211282..49215140,3	MCF-7	breast:
9	chr3:49207496..49209154-chr3:49376769..49379124,2	MCF-7	breast:
10	chr3:49195402..49201533-chr3:49207296..49212401,9	MCF-7	breast:
11	chr3:49156732..49159393-chr3:49207552..49211410,3	K562	blood:

Variant related genes	Relation type
CCDC71	TF binding region
KLHDC8B	TF binding region
ENSG00000172046	Chromatin interaction
ENSG00000114316	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000185909	Chromatin interaction
ENSG00000272434	Chromatin interaction
ENSG00000172037	Chromatin interaction
ENSG00000270441	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000177352	Chromatin interaction
ENSG00000178035	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11717485	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13318132	1.00[EUR][1000 genomes]
rs14828	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1522929	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080495	0.82[ASW][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080510	0.82[ASW][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080567	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1996874	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28615670	1.00[EUR][1000 genomes]
rs4452334	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4527417	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855870	1.00[AMR][1000 genomes]
rs4855872	1.00[EUR][1000 genomes]
rs4855874	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855875	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855876	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855878	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855879	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55808753	1.00[AMR][1000 genomes]
rs55990645	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56101322	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56760510	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56897974	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58914641	1.00[EUR][1000 genomes]
rs58998762	1.00[EUR][1000 genomes]
rs60011446	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60338814	1.00[EUR][1000 genomes]
rs61008775	1.00[EUR][1000 genomes]
rs61744082	1.00[EUR][1000 genomes]
rs61749312	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446270	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446271	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446273	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446276	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6766297	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787665	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6793124	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930094	1.00[EUR][1000 genomes]
rs72931171	1.00[EUR][1000 genomes]
rs72934791	1.00[EUR][1000 genomes]
rs72936804	1.00[EUR][1000 genomes]
rs72936810	1.00[EUR][1000 genomes]
rs72936890	1.00[EUR][1000 genomes]
rs73830703	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830704	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830705	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830706	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833525	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8179172	0.82[ASW][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9811460	1.00[EUR][1000 genomes]
rs9814413	1.00[EUR][1000 genomes]
rs9820609	1.00[EUR][1000 genomes]
rs9833422	1.00[EUR][1000 genomes]
rs9837396	1.00[EUR][1000 genomes]
rs9849446	1.00[EUR][1000 genomes]
rs9861805	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9869504	1.00[EUR][1000 genomes]
rs9877045	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9882714	1.00[EUR][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	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49204400-49208600	Weak transcription	Right Atrium	heart
2	chr3:49204600-49208600	Weak transcription	Aorta	Aorta
3	chr3:49207800-49208600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:49207800-49208600	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr3:49207800-49208600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:49207800-49208600	Enhancers	Placenta	Placenta
7	chr3:49207800-49208600	Enhancers	Gastric	stomach
8	chr3:49207800-49208600	Enhancers	Lung	lung
9	chr3:49207800-49208800	Enhancers	Fetal Heart	heart
10	chr3:49208000-49208600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:49208000-49208600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:49208000-49208600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:49208000-49208600	Enhancers	Primary B cells from peripheral blood	blood
14	chr3:49208000-49208600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr3:49208000-49208600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:49208000-49208600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:49208000-49208600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr3:49208000-49208600	Enhancers	Fetal Brain Male	brain
19	chr3:49208000-49208600	Enhancers	Placenta Amnion	Placenta Amnion
20	chr3:49208000-49208600	Flanking Active TSS	Rectal Smooth Muscle	rectum
21	chr3:49208000-49208600	Enhancers	Spleen	Spleen
22	chr3:49208000-49208600	Flanking Active TSS	HepG2	liver
23	chr3:49208000-49208800	Flanking Active TSS	Fetal Muscle Trunk	muscle
24	chr3:49208000-49208800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr3:49208000-49208800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr3:49208200-49208600	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr3:49208200-49208600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:49208200-49208600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:49208200-49208600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr3:49208200-49208600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:49208200-49208600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:49208200-49208600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:49208200-49208600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:49208200-49208600	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr3:49208200-49208600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr3:49208200-49208600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:49208200-49208600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr3:49208200-49208600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:49208200-49208600	Flanking Active TSS	Brain Anterior Caudate	brain
40	chr3:49208200-49208600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
41	chr3:49208200-49208600	Active TSS	Colonic Mucosa	Colon
42	chr3:49208200-49208600	Flanking Active TSS	Colon Smooth Muscle	Colon
43	chr3:49208200-49208600	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr3:49208200-49208600	Flanking Active TSS	Fetal Brain Female	brain
45	chr3:49208200-49208600	Flanking Active TSS	Fetal Intestine Small	intestine
46	chr3:49208200-49208600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr3:49208200-49208600	Flanking Active TSS	Stomach Mucosa	stomach
48	chr3:49208200-49208600	Enhancers	GM12878-XiMat	blood
49	chr3:49208200-49208600	Flanking Active TSS	HSMM	muscle
50	chr3:49208200-49208600	Flanking Active TSS	K562	blood

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