Variant report

Variant	rs3780560
Chromosome Location	chr9:97866518-97866519
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr9:97684533..97687061-chr9:97864778..97867834,3	MCF-7	breast:
2	chr9:97773273..97775913-chr9:97866060..97867838,2	MCF-7	breast:
3	chr9:97865195..97867947-chr9:97877492..97879411,2	K562	blood:
4	chr9:97529158..97531102-chr9:97866148..97868747,2	MCF-7	breast:
5	chr9:97766132..97767771-chr9:97865819..97868349,2	MCF-7	breast:
6	chr9:97443304..97445720-chr9:97866008..97868131,2	MCF-7	breast:
7	chr9:97863799..97866898-chr9:97878535..97880902,4	MCF-7	breast:
8	chr9:97545172..97548041-chr9:97865707..97867971,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1020962	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1038092	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10761371	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10993471	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12553869	1.00[JPT][hapmap]
rs12555128	1.00[JPT][hapmap]
rs12555829	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1564235	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1571896	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1623009	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16911834	1.00[JPT][hapmap]
rs16911856	1.00[JPT][hapmap]
rs173339	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1871220	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1888944	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1888945	0.80[ASN][1000 genomes]
rs1888946	0.80[ASN][1000 genomes]
rs2061798	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2061801	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2104888	1.00[JPT][hapmap]
rs2306207	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs242448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2655055	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2765817	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs356660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs356661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs356662	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs356663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs356671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs356685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs356686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3739748	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs400727	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4743975	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4743977	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4743978	0.80[ASN][1000 genomes]
rs4743989	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4744421	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4744429	0.80[ASN][1000 genomes]
rs4744437	0.91[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4744440	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs475413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs607105	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs648615	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs651009	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7022963	1.00[JPT][hapmap]
rs7039768	0.80[ASN][1000 genomes]
rs7046900	1.00[JPT][hapmap]
rs72750367	0.80[ASN][1000 genomes]
rs72750373	0.80[ASN][1000 genomes]
rs73540087	0.80[ASN][1000 genomes]
rs9299427	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[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	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
5	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97813000-97873000	Weak transcription	K562	blood
2	chr9:97820600-97875000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr9:97838000-97871200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr9:97844000-97898400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr9:97846200-97880000	Weak transcription	Primary B cells from cord blood	blood
6	chr9:97847600-97878400	Weak transcription	Dnd41	blood
7	chr9:97855000-97867800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr9:97855200-97876800	Weak transcription	GM12878-XiMat	blood
9	chr9:97855400-97884800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr9:97855600-97876400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr9:97855600-97878600	Weak transcription	Stomach Mucosa	stomach
12	chr9:97856200-97872600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:97857800-97869600	Weak transcription	HUVEC	blood vessel
14	chr9:97858600-97867600	Genic enhancers	Fetal Muscle Leg	muscle
15	chr9:97858600-97877200	Strong transcription	Fetal Intestine Large	intestine
16	chr9:97858600-97878400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr9:97858800-97870800	Genic enhancers	Fetal Muscle Trunk	muscle
18	chr9:97860000-97875600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr9:97860200-97867000	Enhancers	Fetal Heart	heart
20	chr9:97860400-97867800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr9:97860400-97879000	Strong transcription	Liver	Liver
22	chr9:97860600-97869000	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr9:97860600-97870200	Strong transcription	Thymus	Thymus
24	chr9:97861000-97869000	Weak transcription	Fetal Thymus	thymus
25	chr9:97861200-97877200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:97861200-97889800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr9:97861600-97866800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr9:97862200-97867200	Enhancers	Brain Substantia Nigra	brain
29	chr9:97862200-97870200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr9:97862600-97869200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr9:97862800-97874000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr9:97863000-97867000	Genic enhancers	Fetal Stomach	stomach
33	chr9:97863000-97867200	Enhancers	Brain Hippocampus Middle	brain
34	chr9:97863000-97869000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr9:97863200-97866800	Enhancers	Rectal Smooth Muscle	rectum
36	chr9:97863200-97867000	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr9:97863200-97869000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr9:97863200-97875600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr9:97863400-97867000	Enhancers	Brain Angular Gyrus	brain
40	chr9:97863400-97867000	Enhancers	Right Atrium	heart
41	chr9:97863400-97867400	Enhancers	Brain Anterior Caudate	brain
42	chr9:97863400-97868000	Weak transcription	NH-A	brain
43	chr9:97863400-97874800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr9:97863600-97866600	Enhancers	Fetal Brain Male	brain
45	chr9:97863600-97868000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr9:97863600-97868000	Weak transcription	Osteobl	bone
47	chr9:97863600-97868400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr9:97863600-97883600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr9:97863800-97867000	Genic enhancers	Right Ventricle	heart
50	chr9:97863800-97867000	Enhancers	HSMM	muscle

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