Variant report

Variant	rs17489748
Chromosome Location	chr3:111448262-111448263
allele	A/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	FOXA1	chr3:111448095-111448347	HepG2	liver:	n/a	n/a
2	NFIC	chr3:111448158-111448890	SK-N-SH	brain:	n/a	n/a
3	MAX	chr3:111448214-111448840	HCT-116	colon:	n/a	n/a
4	TCF12	chr3:111448198-111448947	SK-N-SH	brain:	n/a	n/a
5	MAFK	chr3:111448195-111448370	HepG2	liver:	n/a	n/a
6	GATA3	chr3:111448169-111448866	SK-N-SH	brain:	n/a	n/a
7	FOXA2	chr3:111448068-111448357	HepG2	liver:	n/a	n/a
8	TCF12	chr3:111448203-111448914	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111448045..111449995-chr3:111576976..111579247,2	MCF-7	breast:

Variant related genes	Relation type
PHLDB2	TF binding region
PLCXD2	TF binding region
ENSG00000144824	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12494734	0.86[YRI][hapmap]
rs13061461	0.82[AFR][1000 genomes]
rs13317985	0.80[CEU][hapmap]
rs13321524	0.81[CEU][hapmap]
rs13322494	0.81[CEU][hapmap]
rs1398753	0.85[YRI][hapmap]
rs1398754	0.85[YRI][hapmap]
rs17423838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292518	0.92[YRI][hapmap]
rs4276156	0.81[CEU][hapmap];0.86[YRI][hapmap]
rs4381908	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4390898	0.81[CEU][hapmap]
rs4516581	0.81[CEU][hapmap]
rs56108816	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57161413	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57971051	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60844695	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66539950	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762246	0.81[CEU][hapmap]
rs6762572	0.81[CEU][hapmap]
rs6782513	0.81[CEU][hapmap]
rs6787278	0.80[CEU][hapmap]
rs6789977	0.80[CEU][hapmap]
rs6790521	0.81[CEU][hapmap]
rs6790612	0.81[CEU][hapmap]
rs6790825	0.81[CEU][hapmap]
rs67923296	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6795947	0.81[CEU][hapmap]
rs6800047	0.81[CEU][hapmap]
rs6800922	0.80[CEU][hapmap]
rs6802960	0.81[CEU][hapmap]
rs68057139	0.88[EUR][1000 genomes]
rs7614433	0.80[CEU][hapmap]
rs9842396	0.80[CEU][hapmap]
rs9843288	0.81[CEU][hapmap]
rs9858064	0.81[CEU][hapmap]
rs9858228	0.80[CEU][hapmap]
rs9880633	0.81[CEU][hapmap];0.80[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591290	chr3:111427455-111462570	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111415200-111454200	Weak transcription	Small Intestine	intestine
2	chr3:111420400-111450600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:111427200-111448400	Weak transcription	Right Ventricle	heart
4	chr3:111427600-111456000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:111428800-111451200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:111431600-111451400	Weak transcription	Gastric	stomach
7	chr3:111432000-111448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:111432000-111448600	Weak transcription	Brain Germinal Matrix	brain
9	chr3:111434000-111451200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:111436800-111448400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:111440400-111448400	Weak transcription	Right Atrium	heart
12	chr3:111440800-111451200	Weak transcription	Primary B cells from cord blood	blood
13	chr3:111441400-111448400	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:111441400-111451000	Weak transcription	Fetal Intestine Small	intestine
15	chr3:111441600-111449800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:111441600-111452800	Weak transcription	Placenta	Placenta
17	chr3:111442000-111450000	Weak transcription	Thymus	Thymus
18	chr3:111442000-111452000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:111442000-111454200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr3:111442400-111456000	Weak transcription	Lung	lung
21	chr3:111442600-111448400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:111442600-111451200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:111442800-111448400	Weak transcription	Fetal Stomach	stomach
24	chr3:111442800-111455800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:111443000-111448400	Weak transcription	Left Ventricle	heart
26	chr3:111443000-111448400	Weak transcription	Ovary	ovary
27	chr3:111443000-111448400	Weak transcription	A549	lung
28	chr3:111443200-111454800	Weak transcription	Primary T cells from cord blood	blood
29	chr3:111443400-111448400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:111443800-111448400	Weak transcription	Esophagus	oesophagus
31	chr3:111443800-111451400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:111444000-111448400	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr3:111444200-111456000	Weak transcription	Aorta	Aorta
34	chr3:111444800-111449200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:111445200-111456800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:111446800-111448600	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:111446800-111450200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:111447000-111449600	Enhancers	NH-A	brain
39	chr3:111447200-111448400	Weak transcription	Spleen	Spleen
40	chr3:111447200-111449400	Enhancers	NHEK	skin
41	chr3:111447200-111451200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:111447200-111451800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:111447400-111449600	Enhancers	HSMM	muscle
44	chr3:111447400-111450200	Enhancers	HMEC	breast
45	chr3:111447400-111451000	Weak transcription	Fetal Intestine Large	intestine
46	chr3:111447600-111448400	Weak transcription	Fetal Heart	heart
47	chr3:111447600-111450000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr3:111447600-111451000	Weak transcription	Stomach Mucosa	stomach
49	chr3:111447800-111449000	Enhancers	HUVEC	blood vessel
50	chr3:111447800-111451200	Weak transcription	Duodenum Mucosa	Duodenum

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