Variant report

Variant	rs3789391
Chromosome Location	chr1:94479338-94479339
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	E2F6	chr1:94477037-94479451	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94474811..94477803-chr1:94479025..94480714,3	K562	blood:
2	chr1:94478608..94480498-chr1:94484594..94486437,2	MCF-7	breast:

Variant related genes	Relation type
ABCA4	TF binding region
ENSG00000198691	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10874829	1.00[CEU][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs11165062	0.82[JPT][hapmap]
rs11165063	0.82[JPT][hapmap]
rs12049183	0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17110808	0.87[CEU][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap]
rs17391612	0.82[JPT][hapmap]
rs4147859	0.87[EUR][1000 genomes]
rs4147861	0.87[EUR][1000 genomes]
rs55694362	0.84[EUR][1000 genomes]
rs56166161	0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv516137	chr1:94404238-94504545	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94471200-94480600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:94475400-94485600	Weak transcription	NH-A	brain
3	chr1:94476400-94479400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:94476400-94480000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:94476600-94479400	Enhancers	Placenta	Placenta
6	chr1:94476600-94479600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr1:94476800-94480400	Enhancers	Fetal Intestine Large	intestine
8	chr1:94477000-94479400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
9	chr1:94477000-94479800	Enhancers	Fetal Intestine Small	intestine
10	chr1:94477000-94481600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr1:94477200-94480400	Weak transcription	HMEC	breast
12	chr1:94477400-94479800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
13	chr1:94477400-94480000	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr1:94477400-94480200	Enhancers	Brain Germinal Matrix	brain
15	chr1:94477600-94479400	Enhancers	H9 Cell Line	embryonic stem cell
16	chr1:94477600-94479400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
17	chr1:94477800-94479800	Weak transcription	Spleen	Spleen
18	chr1:94478000-94479600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
19	chr1:94478000-94479800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
20	chr1:94478400-94479600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:94478400-94480000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
22	chr1:94478400-94480400	Weak transcription	Osteobl	bone
23	chr1:94478600-94480000	Bivalent Enhancer	Fetal Muscle Leg	muscle
24	chr1:94478800-94479400	Enhancers	Colonic Mucosa	Colon
25	chr1:94478800-94479400	Enhancers	Placenta Amnion	Placenta Amnion
26	chr1:94478800-94479600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
27	chr1:94479000-94479400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
28	chr1:94479000-94479400	Enhancers	HSMM	muscle
29	chr1:94479000-94479600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
30	chr1:94479000-94479600	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr1:94479000-94480200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:94479000-94481600	Enhancers	K562	blood
33	chr1:94479200-94480200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:94479200-94484800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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