Variant report

Variant	rs2783496
Chromosome Location	chr1:93644738-93644739
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr1:93644469-93647061	GM12878	blood:	n/a	chr1:93645456-93645466
2	GATA1	chr1:93644434-93647154	PBDE	blood:	n/a	n/a
3	RCOR1	chr1:93644724-93644784	K562	blood:	n/a	n/a
4	KAP1	chr1:93644498-93646489	HEK293	kidney:	n/a	n/a
5	MXI1	chr1:93643106-93647204	SK-N-SH	brain:	n/a	n/a
6	GTF3C2	chr1:93644512-93645392	Hela-S3	cervix:	n/a	n/a
7	SIN3A	chr1:93644717-93647046	GM12878	blood:	n/a	n/a
8	CHD1	chr1:93643454-93647252	IMR90	lung:	n/a	chr1:93645456-93645466

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:93643262..93645748-chr1:94311384..94313517,2	K562	blood:
2	chr1:93543004..93547095-chr1:93643826..93649088,10	K562	blood:
3	chr1:93302921..93305469-chr1:93643662..93645581,2	K562	blood:
4	chr1:93643769..93645748-chr1:94311324..94312884,2	K562	blood:
5	chr1:93542817..93546420-chr1:93641583..93645468,3	MCF-7	breast:
6	chr1:93631724..93634968-chr1:93643710..93645431,3	K562	blood:
7	chr1:93592377..93594266-chr1:93643687..93645200,2	K562	blood:
8	chr1:93296314..93299115-chr1:93644282..93648010,4	K562	blood:
9	chr1:16840807..16843778-chr1:93644585..93646473,2	MCF-7	breast:

No data

Variant related genes	Relation type
CCDC18	TF binding region
ENSG00000143033	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000137936	Chromatin interaction
ENSG00000260464	Chromatin interaction
ENSG00000122406	Chromatin interaction
ENSG00000251795	Chromatin interaction
ENSG00000261135	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1010476	0.89[ASN][1000 genomes]
rs10874766	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11164896	0.84[EUR][1000 genomes]
rs11164905	0.84[EUR][1000 genomes]
rs12027142	0.92[EUR][1000 genomes]
rs12033147	0.84[EUR][1000 genomes]
rs12038046	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12045001	0.84[EUR][1000 genomes]
rs12046063	0.92[EUR][1000 genomes]
rs12563709	0.84[EUR][1000 genomes]
rs2255722	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281524	0.88[ASN][1000 genomes]
rs2484486	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2749732	0.80[ASN][1000 genomes]
rs2783490	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2783493	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2783495	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2783497	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2783499	0.85[ASN][1000 genomes]
rs2783500	0.85[ASN][1000 genomes]
rs2783501	0.85[ASN][1000 genomes]
rs2783504	0.83[ASN][1000 genomes]
rs2783505	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2815406	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2815415	0.85[ASN][1000 genomes]
rs2815429	0.86[ASN][1000 genomes]
rs28782525	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2893242	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3904666	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs489183	0.89[ASN][1000 genomes]
rs556446	0.81[ASN][1000 genomes]
rs579138	0.80[ASN][1000 genomes]
rs61799470	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61799496	0.83[ASN][1000 genomes]
rs61799497	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61799517	0.84[EUR][1000 genomes]

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	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers 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	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2783496	DR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93636200-93644800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:93641600-93645000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:93642000-93647000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:93642200-93646800	Active TSS	Hela-S3	cervix
5	chr1:93642200-93647200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:93642400-93645200	Weak transcription	Spleen	Spleen
7	chr1:93642400-93646800	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr1:93642600-93647800	Active TSS	K562	blood
9	chr1:93642800-93647000	Active TSS	Psoas Muscle	Psoas
10	chr1:93642800-93647200	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr1:93643000-93645600	Active TSS	Right Atrium	heart
12	chr1:93643000-93646000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:93643000-93647000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:93643000-93647600	Active TSS	NHLF	lung
15	chr1:93643000-93648400	Active TSS	GM12878-XiMat	blood
16	chr1:93643200-93644800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr1:93643200-93646000	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr1:93643200-93647000	Active TSS	NHDF-Ad	bronchial
19	chr1:93643200-93647400	Active TSS	A549	lung
20	chr1:93643200-93647600	Active TSS	HMEC	breast
21	chr1:93643400-93645200	Active TSS	HepG2	liver
22	chr1:93643400-93645800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:93643400-93646800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:93643400-93646800	Active TSS	Stomach Smooth Muscle	stomach
25	chr1:93643400-93647200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:93643600-93644800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr1:93643600-93644800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr1:93643600-93646600	Active TSS	Ovary	ovary
29	chr1:93643600-93647200	Active TSS	H1 Cell Line	embryonic stem cell
30	chr1:93643600-93647200	Active TSS	H9 Cell Line	embryonic stem cell
31	chr1:93643600-93647400	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr1:93643600-93647600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:93643600-93647800	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr1:93643800-93644800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
35	chr1:93643800-93645200	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr1:93643800-93645400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:93643800-93646600	Active TSS	Aorta	Aorta
38	chr1:93643800-93646800	Active TSS	Right Ventricle	heart
39	chr1:93643800-93647000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr1:93643800-93647000	Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr1:93643800-93647200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:93643800-93647200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:93643800-93647200	Active TSS	Colonic Mucosa	Colon
44	chr1:93644000-93644800	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr1:93644000-93645400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:93644000-93646600	Active TSS	Fetal Intestine Small	intestine
47	chr1:93644000-93646800	Active TSS	Brain Angular Gyrus	brain
48	chr1:93644000-93646800	Active TSS	NH-A	brain
49	chr1:93644000-93647800	Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr1:93644200-93645000	Weak transcription	Placenta Amnion	Placenta Amnion

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