Variant report

Variant	rs6699725
Chromosome Location	chr1:161703525-161703526
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	SP1	chr1:161703229-161703916	HCT-116	colon:	n/a	n/a
2	CEBPB	chr1:161703306-161703781	MCF-7	breast:	n/a	n/a
3	E2F4	chr1:161703379-161703691	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr1:161703333-161703694	MCF-7	breast:	n/a	n/a
5	JUND	chr1:161703233-161703885	HCT-116	colon:	n/a	chr1:161703868-161703880
6	CEBPB	chr1:161703314-161703790	HCT-116	colon:	n/a	n/a
7	CTCF	chr1:161703400-161703550	HPAF	blood vessel:	n/a	n/a
8	JUND	chr1:161703287-161703696	SK-N-SH	brain:	n/a	n/a
9	MAX	chr1:161703347-161703689	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr1:161703339-161703689	HCT-116	colon:	n/a	n/a
11	FOS	chr1:161703303-161703717	HUVEC	blood vessel:	n/a	chr1:161703544-161703555
12	MAX	chr1:161703357-161703696	NB4	blood:	n/a	n/a
13	STAT3	chr1:161703231-161703760	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr1:161703074-161703759	MCF10A-Er-Src	breast:	n/a	chr1:161703544-161703555
15	EGR1	chr1:161703394-161703718	MCF-7	breast:	n/a	n/a
16	STAT3	chr1:161703224-161703739	MCF10A-Er-Src	breast:	n/a	n/a
17	FOS	chr1:161703260-161703745	MCF10A-Er-Src	breast:	n/a	chr1:161703544-161703555
18	GATA2	chr1:161703224-161703599	HUVEC	blood vessel:	n/a	n/a
19	EP300	chr1:161703197-161703834	SK-N-SH	brain:	n/a	chr1:161703787-161703797
20	NFIC	chr1:161703257-161703759	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr1:161703381-161703664	U87	brain:	n/a	n/a
22	YY1	chr1:161703461-161703710	HCT-116	colon:	n/a	n/a
23	MYC	chr1:161703286-161703691	MCF10A-Er-Src	breast:	n/a	n/a
24	STAT3	chr1:161703139-161703776	MCF10A-Er-Src	breast:	n/a	n/a
25	STAT3	chr1:161703285-161703723	MCF10A-Er-Src	breast:	n/a	n/a
26	FOSL2	chr1:161703324-161703656	MCF-7	breast:	n/a	n/a
27	FOSL1	chr1:161703163-161703858	HCT-116	colon:	n/a	n/a
28	CEBPB	chr1:161703263-161703777	IMR90	lung:	n/a	n/a
29	POLR2A	chr1:161703466-161703632	MCF10A-Er-Src	breast:	n/a	n/a
30	CEBPB	chr1:161703188-161703891	HCT-116	colon:	n/a	n/a
31	YY1	chr1:161703321-161703711	SK-N-SH	brain:	n/a	n/a
32	MYC	chr1:161703263-161703737	MCF10A-Er-Src	breast:	n/a	n/a
33	TEAD4	chr1:161703388-161703749	ECC-1	luminal epithelium:	n/a	n/a
34	FOSL2	chr1:161703163-161703820	SK-N-SH	brain:	n/a	n/a
35	TCF12	chr1:161703196-161703748	SK-N-SH	brain:	n/a	n/a
36	GATA3	chr1:161703322-161703697	T-47D	breast:	n/a	n/a
37	FOSL1	chr1:161703242-161703776	HCT-116	colon:	n/a	n/a
38	CEBPB	chr1:161703362-161703726	A549	lung:	n/a	n/a
39	FOS	chr1:161703350-161703737	MCF10A-Er-Src	breast:	n/a	chr1:161703544-161703555
40	FOS	chr1:161703133-161703750	MCF10A-Er-Src	breast:	n/a	chr1:161703544-161703555

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:161703503..161707776-chr1:161717836..161724077,7	K562	blood:
2	chr1:161702286..161705058-chr1:161705873..161710501,6	K562	blood:

Variant related genes	Relation type
RN7SL466P	TF binding region
ENSG00000081721	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10799934	0.92[ASW][hapmap];0.81[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs10917809	0.91[ASW][hapmap];0.81[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs16858733	0.89[CEU][hapmap]
rs6427623	0.81[CEU][hapmap];0.85[GIH][hapmap]
rs7522783	0.93[AFR][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	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS 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	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6699725	INSRR	cis	parietal	SCAN
rs6699725	FCRL6	cis	cerebellum	SCAN
rs6699725	KIRREL	cis	cerebellum	SCAN
rs6699725	RGS4	cis	parietal	SCAN
rs6699725	TMEM79	cis	parietal	SCAN
rs6699725	C1orf66	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161697800-161706600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:161698000-161706000	Enhancers	NHEK	skin
3	chr1:161698000-161707600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:161698400-161704400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:161698600-161705600	Weak transcription	A549	lung
6	chr1:161699200-161704400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:161699200-161707400	Enhancers	HMEC	breast
8	chr1:161700200-161707800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr1:161700200-161708400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:161700600-161705400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:161700600-161705600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:161700600-161706000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:161700600-161706200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:161700800-161705000	Weak transcription	GM12878-XiMat	blood
15	chr1:161700800-161705600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:161700800-161706000	Weak transcription	Hela-S3	cervix
17	chr1:161701000-161706000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:161701400-161704000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:161701400-161706000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:161701800-161705600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:161702600-161704400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:161702600-161704400	Enhancers	Muscle Satellite Cultured Cells	--
23	chr1:161702600-161704600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:161702600-161704600	Enhancers	NHDF-Ad	bronchial
25	chr1:161702800-161704000	Enhancers	HSMM	muscle
26	chr1:161702800-161704000	Enhancers	HUVEC	blood vessel
27	chr1:161702800-161704000	Enhancers	NHLF	lung
28	chr1:161702800-161704200	Enhancers	Osteobl	bone
29	chr1:161703000-161704000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:161703000-161704000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:161703000-161704000	Enhancers	NH-A	brain
32	chr1:161703200-161704000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:161703200-161704000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:161703200-161704000	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr1:161703400-161703600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
36	chr1:161703400-161703600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
37	chr1:161703400-161704000	Bivalent Enhancer	Fetal Lung	lung
38	chr1:161703400-161704200	Weak transcription	HSMMtube	muscle
39	chr1:161703400-161704400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr1:161703400-161706000	Weak transcription	K562	blood

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