Variant report

Variant	rs7763294
Chromosome Location	chr6:140383733-140383734
allele	G/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	RAD21	chr6:140382918-140383949	IMR90	lung:	n/a	n/a
2	GATA3	chr6:140382966-140384242	SH-SY5Y	brain:	n/a	chr6:140383081-140383097 chr6:140383079-140383100 chr6:140384104-140384112 chr6:140383086-140383093 chr6:140383086-140383093 chr6:140383086-140383093
3	MEF2A	chr6:140382988-140384050	SK-N-SH	brain:	n/a	n/a
4	FOXM1	chr6:140382751-140384208	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr6:140382778-140384182	SK-N-MC	brain:	n/a	n/a
6	EP300	chr6:140383166-140384066	MCF-7	breast:	n/a	chr6:140383430-140383444
7	RFX5	chr6:140383002-140383926	Hela-S3	cervix:	n/a	n/a
8	NR2F2	chr6:140383125-140384019	MCF-7	breast:	n/a	n/a
9	GATA3	chr6:140383003-140384092	MCF-7	breast:	n/a	chr6:140383081-140383097 chr6:140383079-140383100 chr6:140383086-140383093 chr6:140383086-140383093 chr6:140383086-140383093
10	EP300	chr6:140382687-140384374	SK-N-SH	brain:	n/a	chr6:140383430-140383444
11	TCF12	chr6:140382774-140384412	SK-N-SH	brain:	n/a	chr6:140383697-140383707 chr6:140383696-140383703
12	PBX3	chr6:140382825-140383923	SK-N-SH	brain:	n/a	n/a
13	FOS	chr6:140383138-140383848	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr6:140383220-140383828	MCF10A-Er-Src	breast:	n/a	n/a
15	JUND	chr6:140382852-140384055	SK-N-SH	brain:	n/a	n/a
16	JUND	chr6:140382855-140384017	SK-N-SH	brain:	n/a	n/a
17	CEBPB	chr6:140383052-140384107	MCF-7	breast:	n/a	n/a
18	GATA3	chr6:140383226-140384131	MCF-7	breast:	n/a	chr6:140384104-140384112
19	TEAD4	chr6:140383520-140383951	MCF-7	breast:	n/a	n/a
20	EP300	chr6:140383567-140383963	SK-N-SH_RA	brain:	n/a	n/a
21	SIN3AK20	chr6:140383067-140384081	MCF-7	breast:	n/a	n/a
22	TCF12	chr6:140383084-140384205	MCF-7	breast:	n/a	chr6:140383697-140383707 chr6:140383696-140383703
23	NR2F2	chr6:140382997-140383984	MCF-7	breast:	n/a	n/a
24	NFIC	chr6:140382792-140384453	SK-N-SH	brain:	n/a	chr6:140383691-140383708
25	STAT3	chr6:140383237-140383773	MCF10A-Er-Src	breast:	n/a	chr6:140383419-140383427
26	SP1	chr6:140382993-140383749	A549	lung:	n/a	n/a
27	CEBPB	chr6:140382383-140383927	Hela-S3	cervix:	n/a	chr6:140382445-140382458
28	FOSL2	chr6:140382961-140383967	SK-N-SH	brain:	n/a	n/a
29	TCF7L2	chr6:140383426-140384007	MCF-7	breast:	n/a	chr6:140383892-140383901
30	SP1	chr6:140383091-140383747	A549	lung:	n/a	n/a
31	MXI1	chr6:140383132-140384023	Hela-S3	cervix:	n/a	n/a
32	RCOR1	chr6:140383040-140383815	Hela-S3	cervix:	n/a	n/a
33	TCF12	chr6:140382811-140384279	SK-N-SH	brain:	n/a	chr6:140383697-140383707 chr6:140383696-140383703
34	RXRA	chr6:140382877-140383958	SK-N-SH	brain:	n/a	n/a
35	NFIC	chr6:140383496-140383986	ECC-1	luminal epithelium:	n/a	chr6:140383691-140383708
36	ZNF217	chr6:140383308-140383962	MCF-7	breast:	n/a	n/a
37	MAX	chr6:140383049-140383820	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr6:140383037-140383866	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr6:140383197-140383982	MCF10A-Er-Src	breast:	n/a	n/a
40	TCF12	chr6:140382971-140383789	A549	lung:	n/a	chr6:140383697-140383707 chr6:140383696-140383703
41	GATA3	chr6:140382978-140383985	A549	lung:	n/a	chr6:140383081-140383097 chr6:140383079-140383100 chr6:140383086-140383093 chr6:140383086-140383093 chr6:140383086-140383093
42	JUND	chr6:140383005-140384109	MCF-7	breast:	n/a	n/a
43	NFIC	chr6:140382945-140384205	SK-N-SH	brain:	n/a	chr6:140383691-140383708
44	TCF7L2	chr6:140383139-140383810	Hela-S3	cervix:	n/a	n/a
45	RAD21	chr6:140383161-140383996	MCF-7	breast:	n/a	n/a
46	RAD21	chr6:140383555-140383785	SK-N-SH_RA	brain:	n/a	n/a
47	CEBPB	chr6:140383239-140383866	MCF-7	breast:	n/a	n/a
48	FOXM1	chr6:140382892-140384320	MCF-7	breast:	n/a	n/a
49	MEF2A	chr6:140382980-140384084	SK-N-SH	brain:	n/a	n/a
50	MYC	chr6:140383153-140383898	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:139692663..139698708-chr6:140381231..140386402,5	MCF-7	breast:
2	chr6:139695333..139696910-chr6:140382949..140384930,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236013	TF binding region
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10434888	0.91[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs10872525	0.87[CHB][hapmap]
rs1119397	0.87[CHB][hapmap];0.93[CHD][hapmap]
rs12660560	0.87[CHB][hapmap]
rs12663480	0.87[CHB][hapmap]
rs13191189	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs17069768	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs35392782	0.81[ASN][1000 genomes]
rs592440	0.85[EUR][1000 genomes]
rs603310	0.85[EUR][1000 genomes]
rs607284	0.85[EUR][1000 genomes]
rs609488	0.83[EUR][1000 genomes]
rs648510	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs650774	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7751165	0.82[AMR][1000 genomes]
rs7758187	0.81[CHB][hapmap]
rs9373256	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs9373259	0.87[CHB][hapmap];0.93[CHD][hapmap]
rs9373261	0.87[CHB][hapmap]
rs9376494	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs9385895	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs9385901	0.82[CHB][hapmap]
rs9385902	0.86[CHB][hapmap]
rs9385903	0.87[CHB][hapmap];0.93[CHD][hapmap]
rs9389741	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs9389767	0.87[CHB][hapmap]
rs9389768	0.87[CHB][hapmap]
rs9399303	0.81[ASN][1000 genomes]
rs9399304	0.91[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs9399308	0.86[CHB][hapmap];0.84[LWK][hapmap];0.88[MKK][hapmap]
rs9403138	0.81[ASN][1000 genomes]
rs9403139	0.81[ASN][1000 genomes]
rs9403140	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9403148	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs9403156	0.87[CHB][hapmap]

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	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1019508	chr6:140317472-140434466	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1022987	chr6:140344229-140463916	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3473486	chr6:140380637-140392373	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
6	esv3473487	chr6:140380684-140392349	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
7	esv3473488	chr6:140380690-140392319	Flanking Active TSS Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
8	esv3473489	chr6:140380774-140392251	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140373600-140384200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:140374200-140383800	Weak transcription	Fetal Brain Female	brain
3	chr6:140375000-140383800	Weak transcription	Brain Germinal Matrix	brain
4	chr6:140379800-140385200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:140380000-140385200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:140380000-140385800	Enhancers	NHDF-Ad	bronchial
7	chr6:140380400-140383800	Enhancers	Muscle Satellite Cultured Cells	--
8	chr6:140380600-140386400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:140380800-140385000	Enhancers	NHLF	lung
10	chr6:140381000-140384600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:140381000-140385200	Enhancers	HSMM	muscle
12	chr6:140381200-140385800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr6:140381800-140385000	Enhancers	Osteobl	bone
14	chr6:140382000-140384400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:140382000-140384600	Enhancers	NHEK	skin
16	chr6:140382200-140384000	Enhancers	HSMMtube	muscle
17	chr6:140382200-140384400	Enhancers	Placenta	Placenta
18	chr6:140382200-140384600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:140382200-140384600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:140382200-140384600	Enhancers	Fetal Lung	lung
21	chr6:140382400-140384800	Enhancers	Adipose Nuclei	Adipose
22	chr6:140382400-140386400	Enhancers	Placenta Amnion	Placenta Amnion
23	chr6:140382600-140384200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr6:140382600-140384400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:140382600-140384800	Enhancers	Fetal Heart	heart
26	chr6:140382800-140384000	Enhancers	Colon Smooth Muscle	Colon
27	chr6:140383000-140384000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr6:140383000-140384000	Enhancers	Stomach Smooth Muscle	stomach
29	chr6:140383000-140384200	Enhancers	Fetal Muscle Leg	muscle
30	chr6:140383000-140384200	Enhancers	HUVEC	blood vessel
31	chr6:140383000-140384400	Enhancers	Fetal Stomach	stomach
32	chr6:140383000-140384600	Enhancers	Fetal Intestine Large	intestine
33	chr6:140383000-140384600	Enhancers	Fetal Kidney	kidney
34	chr6:140383200-140383800	Weak transcription	Aorta	Aorta
35	chr6:140383200-140383800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr6:140383200-140384000	Weak transcription	Psoas Muscle	Psoas
37	chr6:140383200-140384600	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr6:140383200-140384600	Enhancers	Rectal Smooth Muscle	rectum
39	chr6:140383200-140385600	Weak transcription	Ovary	ovary
40	chr6:140383400-140383800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr6:140383400-140383800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:140383400-140383800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:140383400-140383800	Flanking Active TSS	A549	lung
44	chr6:140383400-140383800	Flanking Active TSS	HMEC	breast
45	chr6:140383400-140384400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:140383400-140384400	Enhancers	Fetal Brain Male	brain
47	chr6:140383400-140384600	Enhancers	Fetal Intestine Small	intestine
48	chr6:140383600-140383800	Flanking Active TSS	NH-A	brain
49	chr6:140383600-140384000	Flanking Active TSS	Hela-S3	cervix
50	chr6:140383600-140384200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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