Variant report

Variant	rs3763651
Chromosome Location	chr9:7103816-7103817
allele	C/T
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	chr9:7103786-7103915	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr9:7103772-7104170	HUVEC	blood vessel:	n/a	n/a
3	SP1	chr9:7103715-7104269	A549	lung:	n/a	n/a
4	SETDB1	chr9:7103557-7104313	U2OS	brain:	n/a	n/a
5	TCF12	chr9:7103638-7104363	A549	lung:	n/a	n/a
6	NR3C1	chr9:7103785-7104195	A549	lung:	n/a	n/a
7	FOSL2	chr9:7103696-7104240	A549	lung:	n/a	n/a
8	EP300	chr9:7103703-7104292	A549	lung:	n/a	n/a
9	CEBPB	chr9:7103804-7104189	A549	lung:	n/a	n/a
10	CEBPB	chr9:7103761-7104150	IMR90	lung:	n/a	n/a
11	FOXA2	chr9:7103716-7104309	A549	lung:	n/a	n/a
12	KAP1	chr9:7103391-7104308	U2OS	brain:	n/a	n/a
13	POLR2A	chr9:7103749-7104244	HUVEC	blood vessel:	n/a	n/a
14	FOXA2	chr9:7103806-7104273	A549	lung:	n/a	n/a
15	NR3C1	chr9:7103752-7104301	A549	lung:	n/a	n/a
16	POLR2A	chr9:7103795-7103821	A549	lung:	n/a	n/a
17	FOS	chr9:7103779-7104129	HUVEC	blood vessel:	n/a	chr9:7103965-7103976
18	NR3C1	chr9:7103645-7104346	A549	lung:	n/a	n/a

Variant related genes	Relation type
KDM4C	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10122120	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10491781	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10491782	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1073496	0.88[CEU][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10758825	0.82[YRI][hapmap]
rs10758826	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10758827	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10758828	0.95[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10758829	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10758830	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10758831	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10758832	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10815518	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10815519	0.96[CEU][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs10815520	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10976045	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10976047	0.84[CHB][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10976052	0.92[CEU][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12686272	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1323404	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1323405	0.86[CHB][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1323406	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1323407	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1407863	0.81[YRI][hapmap]
rs1407867	0.92[CEU][hapmap];0.83[AMR][1000 genomes]
rs2025324	0.94[ASW][hapmap];0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3802400	0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3802403	0.86[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4740871	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs4740872	0.82[YRI][hapmap]
rs6477158	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6477159	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6477160	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs6477161	0.86[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.84[ASN][1000 genomes]
rs7021692	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7023759	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7023789	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7028048	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7037866	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7042418	0.82[YRI][hapmap]
rs7048573	0.87[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7858101	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7860305	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.90[LWK][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7862227	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7862711	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7867958	0.96[CEU][hapmap];0.93[CHB][hapmap];0.88[YRI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7869012	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7869317	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7872366	0.87[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7872504	0.96[CEU][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7872625	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9299041	0.92[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][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	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv613259	chr9:7032776-7541338	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1015874	chr9:7048807-7434890	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv539971	chr9:7048807-7434890	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv869932	chr9:7068359-7133384	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv892189	chr9:7091968-7150997	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv892190	chr9:7094860-7186074	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3763651	INSL4	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:7012200-7111200	Weak transcription	Colonic Mucosa	Colon
2	chr9:7061200-7104600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr9:7075600-7105800	Weak transcription	NHLF	lung
4	chr9:7086600-7105600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr9:7088800-7128000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr9:7090200-7104000	Weak transcription	Right Ventricle	heart
7	chr9:7092800-7104200	Weak transcription	Left Ventricle	heart
8	chr9:7095400-7107400	Weak transcription	Fetal Kidney	kidney
9	chr9:7098600-7118000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:7098800-7108400	Weak transcription	HSMMtube	muscle
11	chr9:7099000-7106800	Weak transcription	Hela-S3	cervix
12	chr9:7100800-7120200	Strong transcription	Primary B cells from cord blood	blood
13	chr9:7102600-7104200	Weak transcription	NHDF-Ad	bronchial
14	chr9:7102800-7114000	Strong transcription	Primary T cells from cord blood	blood
15	chr9:7103000-7104000	Enhancers	Fetal Heart	heart
16	chr9:7103000-7105600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:7103000-7106000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr9:7103000-7110200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr9:7103000-7148600	Strong transcription	Primary B cells from peripheral blood	blood
20	chr9:7103200-7104000	Enhancers	H1 Cell Line	embryonic stem cell
21	chr9:7103200-7104000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:7103200-7104000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
23	chr9:7103200-7104200	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr9:7103200-7104200	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr9:7103200-7104200	Enhancers	HUVEC	blood vessel
26	chr9:7103200-7104600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr9:7103200-7104600	Strong transcription	Fetal Thymus	thymus
28	chr9:7103200-7104600	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr9:7103200-7104800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr9:7103200-7104800	Enhancers	Placenta	Placenta
31	chr9:7103200-7105000	Strong transcription	Fetal Intestine Small	intestine
32	chr9:7103200-7105400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr9:7103200-7105800	Strong transcription	Stomach Smooth Muscle	stomach
34	chr9:7103200-7106000	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr9:7103200-7108200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr9:7103200-7108200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr9:7103200-7116200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr9:7103400-7104000	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr9:7103400-7104200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr9:7103400-7104400	Strong transcription	Fetal Muscle Leg	muscle
41	chr9:7103400-7104600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr9:7103400-7105000	Strong transcription	Fetal Stomach	stomach
43	chr9:7103400-7105400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr9:7103400-7105400	Enhancers	Psoas Muscle	Psoas
45	chr9:7103400-7105600	Strong transcription	Thymus	Thymus
46	chr9:7103400-7105800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr9:7103400-7105800	Strong transcription	Liver	Liver
48	chr9:7103400-7105800	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr9:7103400-7106200	Strong transcription	Duodenum Mucosa	Duodenum
50	chr9:7103400-7107200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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