Variant report

Variant	rs17078449
Chromosome Location	chr3:45980673-45980674
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	MYC	chr3:45980383-45980675	MCF10A-Er-Src	breast:	n/a	n/a
2	EBF1	chr3:45980396-45980805	GM12878	blood:	n/a	n/a
3	MAX	chr3:45980274-45980808	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAZ	chr3:45980229-45981014	IMR90	lung:	n/a	n/a
5	RAD21	chr3:45980206-45980678	MCF-7	breast:	n/a	chr3:45980442-45980455 chr3:45980441-45980448 chr3:45980443-45980452 chr3:45980439-45980458
6	RAD21	chr3:45980310-45980698	MCF-7	breast:	n/a	chr3:45980442-45980455 chr3:45980441-45980448 chr3:45980443-45980452 chr3:45980439-45980458
7	SMC3	chr3:45980255-45980674	Hela-S3	cervix:	n/a	chr3:45980440-45980454
8	PML	chr3:45980193-45980771	GM12878	blood:	n/a	n/a
9	CTCF	chr3:45980192-45980913	HCT-116	colon:	n/a	chr3:45980439-45980455 chr3:45980441-45980454 chr3:45980438-45980456 chr3:45980443-45980451 chr3:45980440-45980461
10	CTCF	chr3:45980225-45980677	K562	blood:	n/a	chr3:45980439-45980455 chr3:45980441-45980454 chr3:45980438-45980456 chr3:45980443-45980451 chr3:45980440-45980461
11	RAD21	chr3:45980187-45980720	SK-N-SH_RA	brain:	n/a	chr3:45980442-45980455 chr3:45980441-45980448 chr3:45980443-45980452 chr3:45980439-45980458
12	FOXM1	chr3:45980194-45980726	GM12878	blood:	n/a	n/a
13	MAX	chr3:45980288-45980802	H1-hESC	embryonic stem cell:	n/a	n/a
14	RAD21	chr3:45980057-45980899	SK-N-SH	brain:	n/a	chr3:45980442-45980455 chr3:45980441-45980448 chr3:45980443-45980452 chr3:45980439-45980458
15	CTCF	chr3:45980226-45980679	IMR90	lung:	n/a	chr3:45980439-45980455 chr3:45980441-45980454 chr3:45980438-45980456 chr3:45980443-45980451 chr3:45980440-45980461
16	RAD21	chr3:45980168-45980763	H1-hESC	embryonic stem cell:	n/a	chr3:45980442-45980455 chr3:45980441-45980448 chr3:45980443-45980452 chr3:45980439-45980458
17	RAD21	chr3:45980235-45981090	IMR90	lung:	n/a	chr3:45980442-45980455 chr3:45980441-45980448 chr3:45980443-45980452 chr3:45980439-45980458
18	MAX	chr3:45980285-45980784	K562	blood:	n/a	n/a
19	ATF2	chr3:45980281-45980708	GM12878	blood:	n/a	n/a
20	EGR1	chr3:45980373-45980689	K562	blood:	n/a	chr3:45980519-45980541
21	RAD21	chr3:45980188-45980872	HCT-116	colon:	n/a	chr3:45980442-45980455 chr3:45980441-45980448 chr3:45980443-45980452 chr3:45980439-45980458
22	USF2	chr3:45980309-45980698	Hela-S3	cervix:	n/a	n/a
23	RAD21	chr3:45980177-45980698	A549	lung:	n/a	chr3:45980442-45980455 chr3:45980441-45980448 chr3:45980443-45980452 chr3:45980439-45980458
24	SMC3	chr3:45980265-45980680	K562	blood:	n/a	chr3:45980440-45980454
25	CTCF	chr3:45980244-45980682	H1-hESC	embryonic stem cell:	n/a	chr3:45980439-45980455 chr3:45980441-45980454 chr3:45980438-45980456 chr3:45980443-45980451 chr3:45980440-45980461
26	CTCF	chr3:45980172-45981440	SK-N-SH	brain:	n/a	chr3:45980439-45980455 chr3:45980441-45980454 chr3:45980438-45980456 chr3:45980443-45980451 chr3:45980440-45980461
27	MYC	chr3:45980305-45980809	NB4	blood:	n/a	n/a
28	SMC3	chr3:45980263-45980691	HepG2	liver:	n/a	chr3:45980440-45980454
29	CTCF	chr3:45980313-45980675	GM12892	blood:	n/a	chr3:45980439-45980455 chr3:45980441-45980454 chr3:45980438-45980456 chr3:45980443-45980451 chr3:45980440-45980461
30	WRNIP1	chr3:45980326-45980723	GM12878	blood:	n/a	n/a
31	RAD21	chr3:45980180-45980753	HCT-116	colon:	n/a	chr3:45980442-45980455 chr3:45980441-45980448 chr3:45980443-45980452 chr3:45980439-45980458
32	CTCF	chr3:45980190-45980840	HCT-116	colon:	n/a	chr3:45980439-45980455 chr3:45980441-45980454 chr3:45980438-45980456 chr3:45980443-45980451 chr3:45980440-45980461
33	RAD21	chr3:45980262-45980732	A549	lung:	n/a	chr3:45980442-45980455 chr3:45980441-45980448 chr3:45980443-45980452 chr3:45980439-45980458
34	RCOR1	chr3:45980253-45981616	IMR90	lung:	n/a	n/a
35	MAZ	chr3:45980305-45980673	K562	blood:	n/a	n/a
36	CTCF	chr3:45980620-45980770	GM06990	blood:	n/a	n/a
37	CTCF	chr3:45980294-45980683	MCF-7	breast:	n/a	chr3:45980439-45980455 chr3:45980441-45980454 chr3:45980438-45980456 chr3:45980443-45980451 chr3:45980440-45980461
38	RUNX3	chr3:45980208-45980703	GM12878	blood:	n/a	n/a
39	MAX	chr3:45980234-45980840	H1-hESC	embryonic stem cell:	n/a	n/a
40	RAD21	chr3:45980223-45980691	GM12878	blood:	n/a	chr3:45980442-45980455 chr3:45980441-45980448 chr3:45980443-45980452 chr3:45980439-45980458
41	SMC3	chr3:45980050-45981293	SK-N-SH	brain:	n/a	chr3:45980440-45980454
42	CTCF	chr3:45980030-45980917	A549	lung:	n/a	chr3:45980439-45980455 chr3:45980441-45980454 chr3:45980438-45980456 chr3:45980443-45980451 chr3:45980440-45980461
43	CTCF	chr3:45980220-45980713	GM12878	blood:	n/a	chr3:45980439-45980455 chr3:45980441-45980454 chr3:45980438-45980456 chr3:45980443-45980451 chr3:45980440-45980461
44	MAX	chr3:45980303-45980772	NB4	blood:	n/a	n/a
45	RAD21	chr3:45980142-45980774	ECC-1	luminal epithelium:	n/a	chr3:45980442-45980455 chr3:45980441-45980448 chr3:45980443-45980452 chr3:45980439-45980458
46	SMC3	chr3:45980235-45980739	GM12878	blood:	n/a	chr3:45980440-45980454
47	RAD21	chr3:45980260-45980725	GM12878	blood:	n/a	chr3:45980442-45980455 chr3:45980441-45980448 chr3:45980443-45980452 chr3:45980439-45980458
48	MXI1	chr3:45980196-45980963	IMR90	lung:	n/a	n/a
49	USF1	chr3:45980326-45980679	H1-hESC	embryonic stem cell:	n/a	n/a
50	MAX	chr3:45980346-45980708	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:45979895..45980974-chr3:46119979..46120805,8	MCF-7	breast:
2	chr3:45980083..45981150-chr3:46117757..46119043,6	MCF-7	breast:
3	chr3:45979997..45980877-chr3:46419945..46420540,2	K562	blood:
4	chr3:45979945..45981160-chr3:46119722..46121315,21	K562	blood:
5	chr3:45978760..45981889-chr3:46119716..46121321,25	MCF-7	breast:
6	chr3:45979978..45982491-chr3:46035904..46038054,2	MCF-7	breast:
7	chr3:45980001..45980840-chr3:46121974..46122633,2	K562	blood:
8	chr3:45980561..45981539-chr3:46118125..46119072,2	MCF-7	breast:
9	chr3:45978904..45980774-chr3:45983050..45984937,2	MCF-7	breast:
10	chr3:45979673..45982315-chr3:46020948..46022553,2	K562	blood:

Variant related genes	Relation type
CXCR6	TF binding region
ENSG00000163820	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1072755	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs12054287	0.88[CEU][hapmap]
rs13066048	0.85[CHB][hapmap]
rs1552489	0.90[CHB][hapmap];0.86[CHD][hapmap]
rs17078454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2054866	0.85[CHB][hapmap];0.86[CHD][hapmap]
rs2234351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2234358	0.85[CHB][hapmap];0.88[CHD][hapmap]
rs2248228	0.86[CHB][hapmap]
rs35537559	0.85[EUR][1000 genomes]
rs3774634	0.84[CHB][hapmap]
rs3774638	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3774639	0.85[CHB][hapmap];0.86[CHD][hapmap]
rs3774640	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3796373	0.81[CHD][hapmap]
rs3796376	0.89[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3821883	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4535265	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs4682799	0.90[CHB][hapmap];0.88[CHD][hapmap]
rs4682800	0.89[CHB][hapmap]
rs4683153	0.97[ASN][1000 genomes]
rs4683157	0.81[CHB][hapmap]
rs57204020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59226168	0.83[EUR][1000 genomes]
rs59767267	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60237998	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60779624	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62242787	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62242788	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62242796	0.85[EUR][1000 genomes]
rs62245106	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62245108	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6778225	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6778324	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6781121	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6781668	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6800954	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7623476	0.85[CEU][hapmap]
rs7631809	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7643426	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs936938	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs936939	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45958000-45980800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:45958800-45988000	Weak transcription	HUVEC	blood vessel
3	chr3:45959400-46009800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:45963200-45985200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:45970200-45988200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:45971800-45982400	Weak transcription	NHEK	skin
7	chr3:45972800-45988600	Weak transcription	Small Intestine	intestine
8	chr3:45973400-45986400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:45973800-45988000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:45973800-45991400	Weak transcription	Brain Germinal Matrix	brain
11	chr3:45974400-45988000	Weak transcription	Fetal Kidney	kidney
12	chr3:45976400-45981800	Strong transcription	Fetal Stomach	stomach
13	chr3:45977400-45987000	Weak transcription	Fetal Lung	lung
14	chr3:45977400-45988000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:45977600-45983400	Weak transcription	Primary B cells from cord blood	blood
16	chr3:45977600-45987600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:45978000-45988000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:45978200-45982200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:45978200-45988200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:45978400-45983800	Weak transcription	Spleen	Spleen
21	chr3:45978400-45986600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:45978600-45981200	Genic enhancers	Fetal Thymus	thymus
23	chr3:45978800-45982000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:45978800-45982800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:45978800-45994400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:45979000-45987200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:45979000-45988200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:45979000-45993000	Weak transcription	Stomach Mucosa	stomach
29	chr3:45979200-45981400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:45979200-45987200	Weak transcription	Colonic Mucosa	Colon
31	chr3:45979200-45987800	Weak transcription	Brain Anterior Caudate	brain
32	chr3:45979200-45987800	Weak transcription	HepG2	liver
33	chr3:45979200-45988200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:45979400-45981600	Weak transcription	Fetal Intestine Large	intestine
35	chr3:45979400-45982400	Weak transcription	Hela-S3	cervix
36	chr3:45979400-45983200	Weak transcription	Pancreas	Pancrea
37	chr3:45979600-45981400	Enhancers	HSMMtube	muscle
38	chr3:45979600-45983200	Weak transcription	Esophagus	oesophagus
39	chr3:45979600-45984200	Weak transcription	Liver	Liver
40	chr3:45979800-45981400	Enhancers	HSMM	muscle
41	chr3:45979800-45981800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:45979800-45981800	Weak transcription	Primary T cells from cord blood	blood
43	chr3:45979800-45983200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:45979800-45983600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr3:45979800-45983600	Weak transcription	Gastric	stomach
46	chr3:45980000-45980800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:45980000-45981000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:45980200-45980800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr3:45980200-45980800	Weak transcription	Right Ventricle	heart
50	chr3:45980200-45981000	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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