Variant report

Variant	rs1564235
Chromosome Location	chr9:97816146-97816147
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:97816065-97816261	A549	lung:	n/a	n/a
2	POLR2A	chr9:97816062-97816154	A549	lung:	n/a	n/a
3	POLR2A	chr9:97816119-97816216	A549	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr9:97809451..97811509-chr9:97815332..97819190,3	K562	blood:
2	chr9:97815246..97817675-chr9:97824890..97827452,2	MCF-7	breast:
3	chr9:97810097..97812414-chr9:97813223..97817126,5	MCF-7	breast:
4	chr9:97684569..97686306-chr9:97814006..97816839,2	MCF-7	breast:
5	chr9:97815564..97817505-chr9:97820080..97822608,2	MCF-7	breast:
6	chr9:97814331..97816887-chr9:97827066..97829674,2	MCF-7	breast:
7	chr9:97813946..97816396-chr9:97851072..97855306,4	MCF-7	breast:
8	chr9:97813367..97817167-chr9:97817537..97820356,4	K562	blood:

No data

Variant related genes	Relation type
C9orf3	TF binding region
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1020962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217441	1.00[CEU][hapmap]
rs1038092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732407	1.00[CEU][hapmap]
rs10761362	1.00[CEU][hapmap]
rs10761371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993471	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12553869	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12555128	1.00[JPT][hapmap]
rs12555829	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1542108	1.00[CEU][hapmap]
rs1571896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571897	0.85[CHB][hapmap];0.81[AMR][1000 genomes]
rs16911834	1.00[JPT][hapmap]
rs16911856	1.00[JPT][hapmap]
rs1699499	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1871220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs1888944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888945	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888946	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061799	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2061801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104888	1.00[JPT][hapmap]
rs2306207	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs242448	1.00[JPT][hapmap]
rs356660	1.00[JPT][hapmap]
rs356661	1.00[JPT][hapmap]
rs356685	1.00[JPT][hapmap]
rs356686	1.00[JPT][hapmap]
rs3739748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780560	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4332191	1.00[CEU][hapmap]
rs4743972	1.00[CEU][hapmap]
rs4743975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743976	0.86[CHB][hapmap];0.81[AMR][1000 genomes]
rs4743977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743989	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4744421	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744429	1.00[ASN][1000 genomes]
rs4744437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4744440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs475413	1.00[JPT][hapmap]
rs6479578	1.00[CEU][hapmap]
rs6479589	0.81[AMR][1000 genomes]
rs6479596	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479597	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67134693	0.96[ASN][1000 genomes]
rs7019602	1.00[CEU][hapmap]
rs7022739	0.81[AMR][1000 genomes]
rs7022963	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7023719	1.00[CEU][hapmap]
rs7025100	1.00[CEU][hapmap]
rs7039768	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7046900	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs72750335	0.96[ASN][1000 genomes]
rs72750346	0.96[ASN][1000 genomes]
rs72750351	0.96[ASN][1000 genomes]
rs72750359	0.96[ASN][1000 genomes]
rs72750367	1.00[ASN][1000 genomes]
rs72750373	1.00[ASN][1000 genomes]
rs73540087	1.00[ASN][1000 genomes]
rs7867856	1.00[CEU][hapmap]
rs894426	1.00[CEU][hapmap]
rs9299427	0.83[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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97810000-97816800	Transcr. at gene 5' and 3'	A549	lung
2	chr9:97811400-97820800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:97811600-97817600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:97811600-97817600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr9:97811600-97817800	Weak transcription	Right Ventricle	heart
6	chr9:97812000-97816400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr9:97812400-97817400	Weak transcription	GM12878-XiMat	blood
8	chr9:97812600-97816400	Weak transcription	HUVEC	blood vessel
9	chr9:97812600-97817400	Weak transcription	Adipose Nuclei	Adipose
10	chr9:97812600-97818600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr9:97812800-97816400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:97812800-97816400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:97812800-97816800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr9:97812800-97817600	Weak transcription	Right Atrium	heart
15	chr9:97813000-97816200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:97813000-97816200	Weak transcription	Fetal Intestine Large	intestine
17	chr9:97813000-97816400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr9:97813000-97817800	Weak transcription	Colonic Mucosa	Colon
19	chr9:97813000-97817800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr9:97813000-97817800	Weak transcription	Lung	lung
21	chr9:97813000-97818200	Weak transcription	Stomach Mucosa	stomach
22	chr9:97813000-97819600	Weak transcription	Hela-S3	cervix
23	chr9:97813000-97820600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:97813000-97873000	Weak transcription	K562	blood
25	chr9:97813200-97816400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr9:97813200-97816400	Weak transcription	HSMMtube	muscle
27	chr9:97813200-97817000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr9:97813200-97817400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr9:97813200-97817400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr9:97813200-97817600	Weak transcription	Brain Anterior Caudate	brain
31	chr9:97813200-97817600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr9:97813200-97817800	Weak transcription	Fetal Intestine Small	intestine
33	chr9:97813400-97816200	Weak transcription	NHEK	skin
34	chr9:97813400-97816400	Weak transcription	Fetal Kidney	kidney
35	chr9:97813400-97816400	Weak transcription	HMEC	breast
36	chr9:97813400-97817000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr9:97813400-97817400	Weak transcription	Fetal Muscle Leg	muscle
38	chr9:97813400-97817400	Weak transcription	Placenta	Placenta
39	chr9:97813400-97817400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr9:97813400-97817600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr9:97813400-97817600	Weak transcription	Brain Substantia Nigra	brain
42	chr9:97813400-97817800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr9:97813400-97818400	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr9:97813400-97827200	Genic enhancers	Liver	Liver
45	chr9:97813800-97817800	Weak transcription	Brain Angular Gyrus	brain
46	chr9:97814400-97816400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr9:97814400-97817600	Enhancers	Fetal Lung	lung
48	chr9:97814800-97816200	Genic enhancers	NHDF-Ad	bronchial
49	chr9:97815000-97817600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr9:97815200-97816200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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