Variant report

Variant	rs3892709
Chromosome Location	chr1:226312431-226312432
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:226312380-226312530	RPTEC	kidney:	n/a	n/a
2	RAD21	chr1:226312282-226313427	HCT-116	colon:	n/a	chr1:226313039-226313058 chr1:226313041-226313048
3	RAD21	chr1:226312156-226313635	SK-N-SH	brain:	n/a	chr1:226313039-226313058 chr1:226313041-226313048
4	CTCF	chr1:226312340-226312490	HEK293	kidney:	n/a	n/a
5	CTCF	chr1:226312380-226312530	GM12878	blood:	n/a	n/a
6	CTCF	chr1:226312360-226312510	HFF-Myc	foreskin:	n/a	n/a
7	CTCF	chr1:226312380-226312530	HPAF	blood vessel:	n/a	n/a
8	STAT3	chr1:226311973-226312487	MCF10A-Er-Src	breast:	n/a	chr1:226311985-226311997
9	CTCF	chr1:226311662-226313662	A549	lung:	n/a	chr1:226313041-226313054 chr1:226313039-226313055 chr1:226313038-226313056 chr1:226313040-226313061 chr1:226313043-226313051
10	CTCF	chr1:226312380-226312530	K562	blood:	n/a	n/a

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226247784..226253760-chr1:226305545..226317702,29	MCF-7	breast:
2	chr1:226311060..226314029-chr1:226383239..226385017,2	MCF-7	breast:
3	chr1:226295177..226301855-chr1:226303668..226313005,25	K562	blood:
4	chr1:226308185..226314044-chr1:226494990..226498119,7	K562	blood:
5	chr1:226309825..226313136-chr1:226495411..226498700,3	K562	blood:
6	chr1:226310413..226312487-chr1:226416947..226420256,3	K562	blood:
7	chr1:226311571..226313095-chr1:226593410..226595078,2	K562	blood:
8	chr1:226310978..226313880-chr1:226320034..226321559,2	K562	blood:
9	chr1:226250361..226252761-chr1:226312416..226314743,2	K562	blood:
10	chr1:226307758..226313245-chr1:226372036..226376118,6	MCF-7	breast:
11	chr1:226311771..226313658-chr1:226365752..226368057,2	K562	blood:
12	chr1:226066914..226069709-chr1:226309865..226312651,2	K562	blood:
13	chr1:226308697..226313328-chr1:226386714..226391667,5	K562	blood:
14	chr1:226245827..226258736-chr1:226304107..226314743,27	K562	blood:
15	chr1:226185452..226192151-chr1:226306236..226312570,19	K562	blood:
16	chr1:226312430..226313509-chr1:226384375..226385354,6	K562	blood:
17	chr1:226269903..226273105-chr1:226308746..226312539,4	MCF-7	breast:
18	chr1:226308628..226313084-chr1:226318396..226322185,6	MCF-7	breast:
19	chr1:226182615..226184840-chr1:226309773..226312606,2	K562	blood:
20	chr1:226247680..226258196-chr1:226306136..226315725,36	MCF-7	breast:
21	chr1:226310111..226312814-chr1:226537191..226539857,2	MCF-7	breast:
22	chr1:226295676..226301816-chr1:226302378..226313716,36	MCF-7	breast:
23	chr1:226303513..226307082-chr1:226307356..226312783,6	K562	blood:
24	chr1:226305715..226313141-chr1:226367413..226376964,17	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000270598	TF binding region
ENSG00000223570	Chromatin interaction
ENSG00000182827	Chromatin interaction
ENSG00000183814	Chromatin interaction
ENSG00000272562	Chromatin interaction
ENSG00000163041	Chromatin interaction
ENSG00000143751	Chromatin interaction
ENSG00000225518	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11577282	0.90[JPT][hapmap]
rs12069333	0.95[ASN][1000 genomes]
rs1219671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1877153	0.99[ASN][1000 genomes]
rs1877155	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1877156	0.81[AFR][1000 genomes];0.86[ASN][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	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
3	esv1792510	chr1:226277560-226323824	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv832759	chr1:226303760-226504170	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3892709	ACBD3	cis	normal skin	skin_eQTL
rs3892709	ACBD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226310400-226313600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:226310400-226315200	Weak transcription	HSMMtube	muscle
3	chr1:226310400-226333800	Weak transcription	Small Intestine	intestine
4	chr1:226310600-226312600	Weak transcription	Brain Anterior Caudate	brain
5	chr1:226310600-226312600	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:226310600-226312600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:226310600-226312600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:226310600-226312600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:226310600-226312800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:226310600-226312800	Weak transcription	Brain Angular Gyrus	brain
11	chr1:226310600-226312800	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:226310600-226312800	Weak transcription	Spleen	Spleen
13	chr1:226310600-226313000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:226310600-226313000	Enhancers	HMEC	breast
15	chr1:226310600-226313200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:226310600-226314600	Weak transcription	Lung	lung
17	chr1:226310600-226315000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:226310600-226315200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:226310600-226315200	Weak transcription	NH-A	brain
20	chr1:226310600-226315400	Weak transcription	HSMM	muscle
21	chr1:226310600-226315400	Weak transcription	HUVEC	blood vessel
22	chr1:226310600-226319800	Weak transcription	Right Ventricle	heart
23	chr1:226310600-226322400	Weak transcription	Right Atrium	heart
24	chr1:226310800-226312600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr1:226310800-226312600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:226310800-226312600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:226310800-226312600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:226310800-226312600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr1:226310800-226312600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:226310800-226312600	Weak transcription	Fetal Heart	heart
31	chr1:226310800-226312600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:226310800-226312600	Enhancers	A549	lung
33	chr1:226310800-226312800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:226310800-226312800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:226310800-226312800	Weak transcription	Fetal Brain Male	brain
36	chr1:226310800-226312800	Weak transcription	Fetal Lung	lung
37	chr1:226310800-226313000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr1:226310800-226313200	Enhancers	Primary T cells fromperipheralblood	blood
39	chr1:226310800-226313400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:226310800-226313400	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr1:226310800-226313400	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr1:226310800-226313400	Enhancers	Fetal Intestine Small	intestine
43	chr1:226310800-226313400	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr1:226310800-226313600	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr1:226310800-226313600	Enhancers	H1 Cell Line	embryonic stem cell
46	chr1:226310800-226313600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:226310800-226314600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:226310800-226315200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:226310800-226315200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:226310800-226315400	Weak transcription	Primary T cells from cord blood	blood

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