Variant report

Variant	rs3892375
Chromosome Location	chr1:161054054-161054055
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr1:161052323-161054117	HCT-116	colon:	n/a	n/a
2	SMARCC1	chr1:161053019-161054357	Hela-S3	cervix:	n/a	chr1:161053426-161053435
3	MAX	chr1:161052714-161054419	MCF-7	breast:	n/a	n/a
4	MAZ	chr1:161052825-161054697	IMR90	lung:	n/a	n/a
5	MAX	chr1:161053100-161054134	NB4	blood:	n/a	n/a
6	FOXA1	chr1:161054019-161054290	T-47D	breast:	n/a	n/a
7	SP1	chr1:161052119-161054309	HCT-116	colon:	n/a	chr1:161053384-161053398 chr1:161052189-161052203

No data

(count:6 , 50 per page) page: 1

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

(count:1 , 50 per page) page: 1

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

No data

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

Extended variants
information (count: 9 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11265544	1.00[JPT][hapmap];1.00[LWK][hapmap]
rs11588189	0.82[JPT][hapmap]
rs12116949	0.82[ASW][hapmap];0.83[AMR][1000 genomes]
rs12130871	1.00[JPT][hapmap]
rs1411614	0.84[CHD][hapmap]
rs2516838	0.82[JPT][hapmap]
rs2774279	0.82[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3892375	UHMK1	cis	cerebellum	SCAN
rs3892375	F11R	cis	parietal	SCAN
rs3892375	OR10K1	cis	cerebellum	SCAN
rs3892375	USF1	cis	multi-tissue	Pritchard
rs3892375	PEAR1	cis	cerebellum	SCAN
rs3892375	FCRL1	cis	cerebellum	SCAN
rs3892375	F11R	cis	cerebellum	SCAN

Chromatin state (count:64 , 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	chr1:161051200-161055600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:161052200-161054400	Enhancers	Gastric	stomach
14	chr1:161052200-161058400	Enhancers	Pancreas	Pancrea
15	chr1:161052400-161054200	Enhancers	Lung	lung
16	chr1:161052400-161055400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:161052400-161055400	Enhancers	Fetal Intestine Small	intestine
18	chr1:161052400-161055400	Enhancers	A549	lung
19	chr1:161052400-161055400	Enhancers	NHDF-Ad	bronchial
20	chr1:161052400-161057000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:161052600-161054400	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr1:161052600-161055400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:161052600-161055400	Enhancers	HSMMtube	muscle
24	chr1:161052600-161055400	Enhancers	Osteobl	bone
25	chr1:161052600-161055800	Enhancers	HSMM	muscle
26	chr1:161052600-161056200	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr1:161052600-161056400	Enhancers	K562	blood
28	chr1:161052600-161056600	Enhancers	Fetal Intestine Large	intestine
29	chr1:161052800-161054200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr1:161052800-161054200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr1:161052800-161054400	Enhancers	Colonic Mucosa	Colon
32	chr1:161052800-161055200	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr1:161052800-161055400	Enhancers	NH-A	brain
34	chr1:161052800-161055400	Enhancers	NHLF	lung
35	chr1:161052800-161055600	Enhancers	Muscle Satellite Cultured Cells	--
36	chr1:161052800-161055800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:161052800-161056400	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr1:161053000-161054600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:161053000-161055400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:161053000-161056200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:161053000-161056800	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr1:161053200-161054800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:161053200-161059200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:161053400-161054800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:161053400-161055200	Enhancers	Fetal Lung	lung
46	chr1:161053400-161058600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:161053600-161054200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:161053600-161054400	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr1:161053600-161055000	Flanking Active TSS	Placenta Amnion	Placenta Amnion
50	chr1:161053600-161057400	Flanking Active TSS	Placenta	Placenta

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