Variant report

Variant	rs3892376
Chromosome Location	chr1:161053773-161053774
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	CEBPB	chr1:161053083-161054036	IMR90	lung:	n/a	n/a
2	CEBPB	chr1:161053156-161053810	ECC-1	luminal epithelium:	n/a	n/a
3	NR2F2	chr1:161052979-161053788	MCF-7	breast:	n/a	n/a
4	EP300	chr1:161053168-161053813	ECC-1	luminal epithelium:	n/a	chr1:161053327-161053337
5	GATA3	chr1:161052781-161053846	MCF-7	breast:	n/a	n/a
6	EP300	chr1:161053090-161053788	T-47D	breast:	n/a	chr1:161053327-161053337
7	CEBPB	chr1:161052323-161054117	HCT-116	colon:	n/a	n/a
8	SMARCC1	chr1:161053019-161054357	Hela-S3	cervix:	n/a	chr1:161053426-161053435
9	CEBPB	chr1:161052692-161053980	HCT-116	colon:	n/a	n/a
10	MAX	chr1:161052714-161054419	MCF-7	breast:	n/a	n/a
11	MAX	chr1:161052950-161053791	A549	lung:	n/a	n/a
12	JUN	chr1:161052522-161053776	K562	blood:	n/a	chr1:161053426-161053436 chr1:161053217-161053230 chr1:161053426-161053436 chr1:161053426-161053436 chr1:161053256-161053269 chr1:161053427-161053435 chr1:161053426-161053436 chr1:161053221-161053230
13	NFIC	chr1:161053084-161053783	ECC-1	luminal epithelium:	n/a	chr1:161053726-161053754
14	FOSL2	chr1:161053080-161053797	MCF-7	breast:	n/a	chr1:161053426-161053436 chr1:161053426-161053436 chr1:161053426-161053436 chr1:161053427-161053435 chr1:161053426-161053436 chr1:161053221-161053230
15	FOSL2	chr1:161053088-161053790	MCF-7	breast:	n/a	chr1:161053426-161053436 chr1:161053426-161053436 chr1:161053426-161053436 chr1:161053427-161053435 chr1:161053426-161053436 chr1:161053221-161053230
16	TCF12	chr1:161052912-161053920	ECC-1	luminal epithelium:	n/a	chr1:161053327-161053336
17	GATA3	chr1:161053192-161053931	MCF-7	breast:	n/a	chr1:161053858-161053868
18	CEBPB	chr1:161052959-161053777	MCF-7	breast:	n/a	n/a
19	ELF1	chr1:161053060-161053929	MCF-7	breast:	n/a	n/a
20	CEBPB	chr1:161052979-161053832	A549	lung:	n/a	n/a
21	SIN3AK20	chr1:161052752-161053993	MCF-7	breast:	n/a	n/a
22	NFIC	chr1:161053071-161053837	ECC-1	luminal epithelium:	n/a	chr1:161053726-161053754
23	NR2F2	chr1:161052987-161053849	K562	blood:	n/a	n/a
24	EP300	chr1:161053080-161053895	ECC-1	luminal epithelium:	n/a	chr1:161053327-161053337
25	EP300	chr1:161053112-161053805	MCF-7	breast:	n/a	chr1:161053327-161053337
26	MAZ	chr1:161052825-161054697	IMR90	lung:	n/a	n/a
27	MAX	chr1:161053100-161054134	NB4	blood:	n/a	n/a
28	HDAC2	chr1:161053114-161053839	MCF-7	breast:	n/a	n/a
29	TCF12	chr1:161052896-161053792	A549	lung:	n/a	chr1:161053327-161053336
30	TEAD4	chr1:161053144-161053793	ECC-1	luminal epithelium:	n/a	n/a
31	SP1	chr1:161052119-161054309	HCT-116	colon:	n/a	chr1:161053384-161053398 chr1:161052189-161052203
32	MAX	chr1:161053062-161053862	MCF-7	breast:	n/a	n/a
33	NR2F2	chr1:161053023-161053785	MCF-7	breast:	n/a	n/a
34	CEBPB	chr1:161053034-161053774	MCF-7	breast:	n/a	n/a
35	JUND	chr1:161053035-161053791	MCF-7	breast:	n/a	chr1:161053426-161053436 chr1:161053426-161053436 chr1:161053426-161053436 chr1:161053427-161053435 chr1:161053426-161053436 chr1:161053221-161053230
36	TCF12	chr1:161053070-161053801	ECC-1	luminal epithelium:	n/a	chr1:161053327-161053336
37	JUND	chr1:161053168-161053818	MCF-7	breast:	n/a	chr1:161053426-161053436 chr1:161053426-161053436 chr1:161053426-161053436 chr1:161053427-161053435 chr1:161053426-161053436 chr1:161053221-161053230

No.	Distal block	Cell Line	Cell type
1	chr1:161015304..161016112-chr1:161053054..161053924,2	MCF-7	breast:
2	chr1:161051876..161054238-chr1:161125249..161127981,2	K562	blood:
3	chr1:161052998..161054950-chr1:161128036..161130636,2	MCF-7	breast:
4	chr1:161051697..161056385-chr1:161085679..161090534,7	K562	blood:
5	chr1:160989645..160990508-chr1:161052915..161053846,2	MCF-7	breast:
6	chr1:161052309..161054886-chr1:161086826..161089196,2	MCF-7	breast:
7	chr1:161014972..161017157-chr1:161051557..161054618,4	MCF-7	breast:
8	chr1:161012288..161019472-chr1:161047717..161055328,13	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHDC9-1	chr1:161053627-161054602	NONHSAT007099

Variant related genes	Relation type
ENSG00000228917	TF binding region
ENSG00000224985	Chromatin interaction
ENSG00000143256	Chromatin interaction
ENSG00000158773	Chromatin interaction
ENSG00000143258	Chromatin interaction
ENSG00000158793	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10908822	0.94[ASN][1000 genomes]
rs11265547	0.94[ASN][1000 genomes]
rs11265549	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12142854	0.92[ASN][1000 genomes]
rs12401309	1.00[ASW][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1467742	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1556257	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3820097	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4233364	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4656285	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs4656287	0.91[MEX][hapmap]
rs4656288	0.82[MEX][hapmap]
rs4656978	1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs6671492	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	esv988172	chr1:161051918-161055508	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3892376	F11R	cis	cerebellum	SCAN
rs3892376	RXFP4	cis	parietal	SCAN
rs3892376	NIT1	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161039600-161066800	Weak transcription	Right Atrium	heart
2	chr1:161049000-161055000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:161049200-161055600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:161049400-161056400	Enhancers	HMEC	breast
5	chr1:161049400-161056600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:161049600-161054600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr1:161049800-161054600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:161050000-161057800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:161050200-161055800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:161051000-161054800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:161051000-161055800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:161051200-161053800	Enhancers	Stomach Mucosa	stomach
13	chr1:161051200-161055600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:161052200-161054400	Enhancers	Gastric	stomach
15	chr1:161052200-161058400	Enhancers	Pancreas	Pancrea
16	chr1:161052400-161054200	Enhancers	Lung	lung
17	chr1:161052400-161055400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:161052400-161055400	Enhancers	Fetal Intestine Small	intestine
19	chr1:161052400-161055400	Enhancers	A549	lung
20	chr1:161052400-161055400	Enhancers	NHDF-Ad	bronchial
21	chr1:161052400-161057000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:161052600-161054400	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr1:161052600-161055400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:161052600-161055400	Enhancers	HSMMtube	muscle
25	chr1:161052600-161055400	Enhancers	Osteobl	bone
26	chr1:161052600-161055800	Enhancers	HSMM	muscle
27	chr1:161052600-161056200	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr1:161052600-161056400	Enhancers	K562	blood
29	chr1:161052600-161056600	Enhancers	Fetal Intestine Large	intestine
30	chr1:161052800-161053800	Enhancers	H1 Cell Line	embryonic stem cell
31	chr1:161052800-161053800	Flanking Active TSS	Hela-S3	cervix
32	chr1:161052800-161053800	Flanking Active TSS	NHEK	skin
33	chr1:161052800-161054200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr1:161052800-161054200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr1:161052800-161054400	Enhancers	Colonic Mucosa	Colon
36	chr1:161052800-161055200	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr1:161052800-161055400	Enhancers	NH-A	brain
38	chr1:161052800-161055400	Enhancers	NHLF	lung
39	chr1:161052800-161055600	Enhancers	Muscle Satellite Cultured Cells	--
40	chr1:161052800-161055800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:161052800-161056400	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr1:161053000-161053800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:161053000-161054600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:161053000-161055400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:161053000-161056200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:161053000-161056800	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr1:161053200-161054000	Enhancers	Duodenum Mucosa	Duodenum
48	chr1:161053200-161054800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:161053200-161059200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:161053400-161053800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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