Variant report

Variant	rs3780554
Chromosome Location	chr9:97365985-97365986
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97365733..97367940-chr9:97370951..97372481,2	MCF-7	breast:
2	chr9:97363454..97366255-chr9:97375188..97377706,2	K562	blood:
3	chr9:97314619..97316650-chr9:97365797..97368541,2	K562	blood:
4	chr9:97365760..97367307-chr9:97368033..97370545,2	MCF-7	breast:
5	chr9:97343362..97346038-chr9:97364705..97367422,2	MCF-7	breast:
6	chr9:97364234..97367313-chr9:97400419..97403811,3	MCF-7	breast:
7	chr9:97315259..97318533-chr9:97363918..97367292,6	MCF-7	breast:
8	chr9:97315954..97317385-chr9:97365147..97366042,4	MCF-7	breast:
9	chr9:97315606..97319704-chr9:97363491..97367544,5	MCF-7	breast:
10	chr9:97365715..97366434-chr9:97385051..97385749,2	MCF-7	breast:
11	chr9:97316090..97317268-chr9:97365275..97366675,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000165140	Chromatin interaction
ENSG00000231806	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10114605	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10123016	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10123666	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10761345	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10761347	0.82[CEU][hapmap]
rs10761348	0.96[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs10821375	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10993267	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10993269	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs10993271	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs10993276	0.82[CEU][hapmap]
rs1410972	0.96[CEU][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs3739747	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3780555	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4129220	0.82[CEU][hapmap]
rs4744360	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs6479557	0.82[CHD][hapmap]
rs7031924	0.92[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][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	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	esv1840205	chr9:97202200-97366400	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
4	nsv466436	chr9:97343620-97369149	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv614917	chr9:97343620-97369149	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3780554	PHF2	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97347600-97374000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr9:97351800-97369200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:97358000-97368800	Weak transcription	Gastric	stomach
4	chr9:97362600-97367000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr9:97363400-97366000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr9:97364400-97382800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr9:97364800-97382800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr9:97365000-97375400	Genic enhancers	Fetal Intestine Small	intestine
9	chr9:97365000-97376200	Genic enhancers	Liver	Liver
10	chr9:97365200-97367000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr9:97365200-97369200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:97365400-97366000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr9:97365400-97366000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr9:97365400-97366000	Enhancers	Primary hematopoietic stem cells	blood
15	chr9:97365400-97366000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr9:97365400-97366200	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr9:97365400-97366200	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr9:97365400-97366400	Enhancers	Adipose Nuclei	Adipose
19	chr9:97365400-97366400	Enhancers	Fetal Lung	lung
20	chr9:97365400-97366400	Enhancers	Stomach Mucosa	stomach
21	chr9:97365400-97366600	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr9:97365400-97366800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:97365400-97366800	Enhancers	Fetal Intestine Large	intestine
24	chr9:97365400-97368800	Enhancers	Colonic Mucosa	Colon
25	chr9:97365600-97366000	Enhancers	Primary B cells from peripheral blood	blood
26	chr9:97365600-97366000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
27	chr9:97365600-97366000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr9:97365600-97366000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr9:97365600-97366000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr9:97365600-97366000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr9:97365600-97366000	Active TSS	Brain Anterior Caudate	brain
32	chr9:97365600-97366000	Enhancers	Brain Hippocampus Middle	brain
33	chr9:97365600-97366000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
34	chr9:97365600-97366000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr9:97365600-97366200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
36	chr9:97365600-97366200	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr9:97365600-97366200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr9:97365600-97366200	Flanking Active TSS	HepG2	liver
39	chr9:97365600-97366400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr9:97365600-97366400	Enhancers	Duodenum Mucosa	Duodenum
41	chr9:97365600-97366400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr9:97365600-97366800	Enhancers	Fetal Stomach	stomach
43	chr9:97365600-97367200	Enhancers	Fetal Muscle Leg	muscle
44	chr9:97365800-97366000	Enhancers	H1 Cell Line	embryonic stem cell
45	chr9:97365800-97366000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr9:97365800-97366000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:97365800-97366000	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr9:97365800-97366000	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr9:97365800-97366000	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr9:97365800-97366000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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