Variant report

Variant	rs2104888
Chromosome Location	chr9:97702280-97702281
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97701029..97702557-chr9:97765376..97768237,2	MCF-7	breast:
2	chr9:97701079..97703589-chr9:97706608..97709987,3	K562	blood:
3	chr9:97702032..97704710-chr9:97710037..97711547,2	K562	blood:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1020962	1.00[JPT][hapmap]
rs1038092	1.00[JPT][hapmap]
rs10761371	1.00[JPT][hapmap]
rs10993471	1.00[JPT][hapmap]
rs12552838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs12553869	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs12554454	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12555128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12555829	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1382411	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1382412	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1564235	1.00[JPT][hapmap]
rs1571896	1.00[JPT][hapmap]
rs16911834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16911856	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16911862	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1871220	1.00[JPT][hapmap]
rs1888944	1.00[JPT][hapmap]
rs2061798	1.00[JPT][hapmap]
rs2061801	1.00[JPT][hapmap]
rs2306207	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs35322834	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3739748	1.00[JPT][hapmap]
rs3780560	1.00[JPT][hapmap]
rs41316526	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743975	1.00[JPT][hapmap]
rs4743977	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs4743989	1.00[JPT][hapmap]
rs4744421	1.00[JPT][hapmap]
rs4744437	1.00[JPT][hapmap]
rs4744440	1.00[JPT][hapmap]
rs6479578	0.81[AMR][1000 genomes]
rs66642068	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66863985	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67756624	0.90[AMR][1000 genomes]
rs7022963	1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7046900	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs72748596	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748601	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750335	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72750346	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73538177	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7867856	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv1045849	chr9:97688810-97741336	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97660800-97702400	Weak transcription	Primary B cells from cord blood	blood
2	chr9:97670600-97766000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr9:97682000-97713800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr9:97684800-97711000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:97685200-97714600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr9:97687000-97714000	Weak transcription	Thymus	Thymus
7	chr9:97689800-97702600	Weak transcription	Fetal Intestine Large	intestine
8	chr9:97691400-97703400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr9:97691800-97710800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr9:97692200-97713000	Weak transcription	Primary T cells from cord blood	blood
11	chr9:97692400-97707600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr9:97693200-97703000	Weak transcription	Pancreas	Pancrea
13	chr9:97693400-97712600	Weak transcription	Gastric	stomach
14	chr9:97695600-97702400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr9:97695600-97703000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:97695600-97703000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr9:97695600-97709000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr9:97697800-97703000	Weak transcription	Spleen	Spleen
19	chr9:97698400-97702600	Weak transcription	Fetal Intestine Small	intestine
20	chr9:97699000-97703000	Weak transcription	Adipose Nuclei	Adipose
21	chr9:97699200-97703200	Weak transcription	Fetal Kidney	kidney
22	chr9:97699600-97703600	Weak transcription	Fetal Lung	lung
23	chr9:97699800-97702400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr9:97699800-97702600	Weak transcription	Right Atrium	heart
25	chr9:97699800-97703000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:97699800-97703000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr9:97699800-97703000	Weak transcription	Colonic Mucosa	Colon
28	chr9:97699800-97703000	Weak transcription	Esophagus	oesophagus
29	chr9:97699800-97706400	Weak transcription	Brain Angular Gyrus	brain
30	chr9:97700000-97702800	Weak transcription	Small Intestine	intestine
31	chr9:97700000-97703000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr9:97700000-97703000	Weak transcription	Ovary	ovary
33	chr9:97700000-97703000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr9:97700000-97703000	Weak transcription	Right Ventricle	heart
35	chr9:97700000-97703000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr9:97700000-97703000	Strong transcription	HSMM	muscle
37	chr9:97700000-97703400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr9:97700200-97703000	Weak transcription	Brain Anterior Caudate	brain
39	chr9:97700200-97703400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr9:97700200-97703600	Weak transcription	HMEC	breast
41	chr9:97700200-97707200	Weak transcription	Brain Hippocampus Middle	brain
42	chr9:97700200-97707400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr9:97700200-97707400	Weak transcription	Brain Substantia Nigra	brain
44	chr9:97700200-97707600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr9:97700200-97707600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr9:97700200-97707800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr9:97700200-97708200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr9:97700200-97714600	Weak transcription	Fetal Stomach	stomach
49	chr9:97700200-97718600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr9:97700400-97707200	Weak transcription	Brain Inferior Temporal Lobe	brain

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