Variant report

Variant	rs730983
Chromosome Location	chr3:46028056-46028057
allele	C/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	FOXA1	chr3:46027412-46028269	HepG2	liver:	n/a	n/a
2	TEAD4	chr3:46027672-46028245	HepG2	liver:	n/a	n/a
3	ATF1	chr3:46027941-46028138	K562	blood:	n/a	n/a
4	MAX	chr3:46027647-46028295	MCF-7	breast:	n/a	n/a
5	MAX	chr3:46027588-46028207	A549	lung:	n/a	n/a
6	MXI1	chr3:46027673-46028301	HepG2	liver:	n/a	n/a
7	SP1	chr3:46027669-46028283	A549	lung:	n/a	n/a
8	JUND	chr3:46027935-46028140	HepG2	liver:	n/a	chr3:46028030-46028038 chr3:46028028-46028039
9	FOS	chr3:46027877-46028176	MCF10A-Er-Src	breast:	n/a	chr3:46028030-46028038 chr3:46028028-46028039
10	POLR2A	chr3:46027797-46028212	U87	brain:	n/a	n/a
11	STAT3	chr3:46027899-46028070	MCF10A-Er-Src	breast:	n/a	chr3:46027948-46027956
12	JUND	chr3:46027781-46028190	HepG2	liver:	n/a	chr3:46028030-46028038 chr3:46028028-46028039
13	MEF2A	chr3:46027750-46028122	K562	blood:	n/a	chr3:46027996-46028017 chr3:46028001-46028010 chr3:46027996-46028017 chr3:46027999-46028010 chr3:46027998-46028012 chr3:46027997-46028013 chr3:46027998-46028013
14	FOS	chr3:46027871-46028194	MCF10A-Er-Src	breast:	n/a	chr3:46028030-46028038 chr3:46028028-46028039
15	FOXA1	chr3:46027741-46028147	T-47D	breast:	n/a	n/a
16	FOS	chr3:46027885-46028200	HUVEC	blood vessel:	n/a	chr3:46028030-46028038 chr3:46028028-46028039
17	POLR2A	chr3:46027774-46028212	U87	brain:	n/a	n/a
18	MAFK	chr3:46027832-46028153	HepG2	liver:	n/a	n/a
19	JUND	chr3:46027832-46028212	HepG2	liver:	n/a	chr3:46028030-46028038 chr3:46028028-46028039
20	MAX	chr3:46027699-46028317	HepG2	liver:	n/a	n/a
21	FOSL2	chr3:46027661-46028300	A549	lung:	n/a	chr3:46028030-46028038 chr3:46028027-46028038
22	MAX	chr3:46027538-46028307	MCF-7	breast:	n/a	n/a
23	FOXA1	chr3:46027687-46028198	HepG2	liver:	n/a	n/a
24	FOXA2	chr3:46027813-46028288	A549	lung:	n/a	n/a
25	FOS	chr3:46028016-46028077	MCF10A-Er-Src	breast:	n/a	chr3:46028030-46028038 chr3:46028028-46028039
26	MBD4	chr3:46027657-46028182	HepG2	liver:	n/a	n/a
27	FOSL2	chr3:46027823-46028116	A549	lung:	n/a	chr3:46028030-46028038 chr3:46028027-46028038
28	TBP	chr3:46027689-46028167	HepG2	liver:	n/a	n/a
29	FOSL2	chr3:46027781-46028162	MCF-7	breast:	n/a	chr3:46028030-46028038 chr3:46028027-46028038
30	RFX5	chr3:46027802-46028241	HepG2	liver:	n/a	n/a
31	FOSL2	chr3:46027814-46028231	MCF-7	breast:	n/a	chr3:46028030-46028038 chr3:46028027-46028038
32	GATA3	chr3:46027549-46028274	MCF-7	breast:	n/a	n/a
33	FOXA1	chr3:46027780-46028181	T-47D	breast:	n/a	n/a
34	FOXA2	chr3:46027752-46028140	HepG2	liver:	n/a	n/a
35	FOSL2	chr3:46027696-46028289	HepG2	liver:	n/a	chr3:46028030-46028038 chr3:46028027-46028038
36	MAX	chr3:46027575-46028303	HepG2	liver:	n/a	n/a
37	EP300	chr3:46027708-46028124	HepG2	liver:	n/a	chr3:46028036-46028046
38	MAX	chr3:46027531-46028348	A549	lung:	n/a	n/a
39	MXI1	chr3:46027214-46028786	IMR90	lung:	n/a	n/a
40	MYC	chr3:46027741-46028142	MCF10A-Er-Src	breast:	n/a	n/a
41	MYBL2	chr3:46027745-46028235	HepG2	liver:	n/a	n/a
42	MAX	chr3:46027765-46028165	A549	lung:	n/a	n/a
43	CHD2	chr3:46027724-46028233	HepG2	liver:	n/a	n/a
44	EP300	chr3:46027731-46028103	T-47D	breast:	n/a	chr3:46028036-46028046
45	FOXA1	chr3:46027632-46028340	HepG2	liver:	n/a	n/a
46	EP300	chr3:46027932-46028189	HepG2	liver:	n/a	chr3:46028036-46028046
47	TCF12	chr3:46027631-46028271	A549	lung:	n/a	n/a
48	JUN	chr3:46027898-46028193	HepG2	liver:	n/a	chr3:46028030-46028038
49	MYC	chr3:46027830-46028103	MCF10A-Er-Src	breast:	n/a	n/a
50	GATA3	chr3:46027768-46028101	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:46021917..46024700-chr3:46027716..46030169,2	MCF-7	breast:
2	chr3:46008363..46011066-chr3:46026720..46029201,2	MCF-7	breast:
3	chr3:46028019..46029570-chr3:46035343..46037600,2	MCF-7	breast:
4	chr3:46026501..46029475-chr3:46032165..46035137,4	MCF-7	breast:

Variant related genes	Relation type
FYCO1	TF binding region
ENSG00000163820	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1072755	0.96[CEU][hapmap]
rs11130080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12485978	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs12495073	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12630101	0.96[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12635494	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12635657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639598	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13060901	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs13066048	0.96[CEU][hapmap]
rs13073861	0.89[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs1392290	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1392291	0.91[ASN][1000 genomes]
rs1491959	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1500005	0.80[ASN][1000 genomes]
rs1546077	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1552489	0.96[CEU][hapmap]
rs1601867	0.81[ASN][1000 genomes]
rs17078495	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994490	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2054866	0.96[CEU][hapmap];0.82[ASN][1000 genomes]
rs2131091	0.88[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2234358	0.81[ASN][1000 genomes]
rs2248228	1.00[CEU][hapmap]
rs2373154	0.96[CEU][hapmap];0.85[CHB][hapmap]
rs28808964	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34381514	0.80[ASN][1000 genomes]
rs35465473	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35537559	1.00[ASN][1000 genomes]
rs3733097	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3733100	0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3733103	0.88[CEU][hapmap]
rs3774634	0.96[CEU][hapmap]
rs3774639	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs3796375	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3821883	0.83[ASN][1000 genomes]
rs3821884	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3851347	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4234452	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4333119	0.80[ASN][1000 genomes]
rs4535265	0.96[CEU][hapmap]
rs4682800	0.85[JPT][hapmap]
rs4682810	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4683148	0.92[CEU][hapmap]
rs4683156	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4683157	0.96[CEU][hapmap];0.80[ASN][1000 genomes]
rs59226168	1.00[ASN][1000 genomes]
rs60539039	0.89[ASN][1000 genomes]
rs62242796	1.00[ASN][1000 genomes]
rs67044455	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6764042	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6778896	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780163	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6781668	0.83[ASN][1000 genomes]
rs6795629	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs6805094	0.83[ASN][1000 genomes]
rs6809381	0.85[CHB][hapmap]
rs7129	0.88[CEU][hapmap]
rs737452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs751552	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs751553	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7616464	0.80[ASN][1000 genomes]
rs7623460	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7643426	0.84[CHB][hapmap]
rs931704	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs936938	0.96[CEU][hapmap]
rs9824886	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs9831315	0.92[CEU][hapmap]
rs9849015	0.81[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	esv2756987	chr3:46016464-46120400	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2759145	chr3:46016464-46120400	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs730983	CXCR6	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46000000-46029600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:46010200-46029600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:46010200-46033000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:46013600-46034000	Genic enhancers	Fetal Thymus	thymus
5	chr3:46019400-46030000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:46020000-46034200	Genic enhancers	Dnd41	blood
7	chr3:46021400-46028200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:46021400-46036200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:46021600-46034000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:46023000-46029800	Strong transcription	Primary T cells from cord blood	blood
11	chr3:46023200-46028200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:46025000-46029400	Genic enhancers	Fetal Intestine Small	intestine
13	chr3:46025000-46031600	Weak transcription	Fetal Kidney	kidney
14	chr3:46025200-46031800	Enhancers	Right Atrium	heart
15	chr3:46025600-46032400	Enhancers	Stomach Mucosa	stomach
16	chr3:46025600-46033000	Enhancers	Right Ventricle	heart
17	chr3:46025800-46028400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:46025800-46031200	Enhancers	HSMMtube	muscle
19	chr3:46026000-46028200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:46026000-46028800	Enhancers	Aorta	Aorta
21	chr3:46026000-46031800	Enhancers	NHDF-Ad	bronchial
22	chr3:46026200-46028600	Enhancers	Brain Germinal Matrix	brain
23	chr3:46026200-46029800	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr3:46026200-46031800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr3:46026200-46032000	Enhancers	Ovary	ovary
26	chr3:46026200-46032000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr3:46026200-46032000	Enhancers	NHLF	lung
28	chr3:46026400-46028200	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr3:46026400-46028400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr3:46026400-46029200	Enhancers	Adipose Nuclei	Adipose
31	chr3:46026400-46029400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr3:46026400-46029400	Enhancers	Fetal Lung	lung
33	chr3:46026400-46031400	Enhancers	HSMM	muscle
34	chr3:46026400-46031600	Enhancers	Fetal Intestine Large	intestine
35	chr3:46026400-46031800	Enhancers	Fetal Muscle Leg	muscle
36	chr3:46026400-46033800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:46026400-46034600	Genic enhancers	Primary T cells fromperipheralblood	blood
38	chr3:46026600-46028200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:46026600-46028800	Enhancers	Fetal Muscle Trunk	muscle
40	chr3:46026600-46029200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:46026600-46029400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:46026600-46029600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:46026600-46029800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:46026600-46030000	Enhancers	Colonic Mucosa	Colon
45	chr3:46026600-46031400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:46026600-46031400	Enhancers	Lung	lung
47	chr3:46026600-46031600	Enhancers	Pancreas	Pancrea
48	chr3:46026600-46031800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:46026600-46032200	Enhancers	Liver	Liver
50	chr3:46026600-46032200	Enhancers	Duodenum Mucosa	Duodenum

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