Variant report

Variant	rs9817904
Chromosome Location	chr3:151178708-151178709
allele	A/G
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	NFYB	chr3:151178652-151178914	K562	blood:	n/a	chr3:151178745-151178760 chr3:151178745-151178760 chr3:151178742-151178757
2	NFYB	chr3:151178667-151178831	Hela-S3	cervix:	n/a	chr3:151178745-151178760 chr3:151178745-151178760 chr3:151178742-151178757
3	CHD2	chr3:151178632-151178768	Hela-S3	cervix:	n/a	n/a
4	E2F6	chr3:151178579-151179063	H1-hESC	embryonic stem cell:	n/a	n/a
5	RAD21	chr3:151178563-151179200	H1-hESC	embryonic stem cell:	n/a	n/a
6	USF1	chr3:151178552-151178854	H1-hESC	embryonic stem cell:	n/a	n/a
7	HDAC2	chr3:151178451-151179118	MCF-7	breast:	n/a	chr3:151179072-151179086 chr3:151178520-151178534 chr3:151178838-151178852
8	USF1	chr3:151178610-151178961	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:151176832..151178864-chr3:151180710..151183596,2	K562	blood:
2	chr3:151171469..151173239-chr3:151178441..151180540,2	MCF-7	breast:

Variant related genes	Relation type
IGSF10	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1491975	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1491976	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2172248	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4234322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4435614	0.94[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4680440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4680442	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6769246	0.92[ASN][1000 genomes]
rs6774093	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6798252	0.93[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs7610769	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7619322	0.94[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs7621591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9289838	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9812989	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9824609	0.94[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs9825817	0.83[ASN][1000 genomes]
rs9843590	0.84[JPT][hapmap];0.82[EUR][1000 genomes]
rs9858311	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9863400	0.83[ASN][1000 genomes]
rs9871952	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9877298	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829757	chr3:151044880-151226442	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1000355	chr3:151108859-151243835	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv995048	chr3:151114074-151560019	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv877649	chr3:151147968-151236562	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv877650	chr3:151174010-151314449	Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151177200-151179200	Active TSS	Brain Hippocampus Middle	brain
2	chr3:151177200-151179200	Active TSS	Right Atrium	heart
3	chr3:151177600-151178800	Active TSS	Stomach Smooth Muscle	stomach
4	chr3:151177800-151179200	Active TSS	Ovary	ovary
5	chr3:151177800-151179400	Flanking Active TSS	Dnd41	blood
6	chr3:151178000-151178800	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr3:151178000-151179200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
8	chr3:151178000-151179200	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr3:151178000-151179200	Active TSS	Rectal Smooth Muscle	rectum
10	chr3:151178000-151179200	Active TSS	Hela-S3	cervix
11	chr3:151178200-151178800	Active TSS	Duodenum Mucosa	Duodenum
12	chr3:151178200-151179000	Active TSS	Brain Germinal Matrix	brain
13	chr3:151178200-151179000	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr3:151178200-151179200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr3:151178200-151179200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr3:151178200-151179200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr3:151178200-151179200	Active TSS	Fetal Lung	lung
18	chr3:151178200-151179200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
19	chr3:151178400-151178800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
20	chr3:151178400-151178800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:151178400-151178800	Active TSS	Brain Anterior Caudate	brain
22	chr3:151178400-151178800	Active TSS	Brain Cingulate Gyrus	brain
23	chr3:151178400-151179000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:151178400-151179000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:151178400-151179000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:151178400-151179000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr3:151178400-151179000	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr3:151178400-151179000	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr3:151178400-151179000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:151178400-151179000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:151178400-151179000	Active TSS	Fetal Thymus	thymus
32	chr3:151178400-151179000	Active TSS	Right Ventricle	heart
33	chr3:151178400-151179000	Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr3:151178400-151179000	Active TSS	A549	lung
35	chr3:151178400-151179000	Bivalent/Poised TSS	Osteobl	bone
36	chr3:151178400-151179200	Active TSS	H9 Cell Line	embryonic stem cell
37	chr3:151178400-151179200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
38	chr3:151178400-151179200	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr3:151178400-151179200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr3:151178400-151179200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:151178400-151179200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:151178400-151179200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:151178400-151179200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:151178400-151179200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:151178400-151179200	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr3:151178400-151179200	Active TSS	Colon Smooth Muscle	Colon
47	chr3:151178400-151179200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
48	chr3:151178400-151179200	Active TSS	Fetal Kidney	kidney
49	chr3:151178400-151179200	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
50	chr3:151178400-151179200	Active TSS	Thymus	Thymus

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