Variant report

Variant	rs12378396
Chromosome Location	chr9:101765187-101765188
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101760174..101761965-chr9:101764160..101766601,2	K562	blood:
2	chr9:101763772..101766220-chr9:101865272..101867903,2	MCF-7	breast:
3	chr9:101760174..101763909-chr9:101764160..101767138,3	K562	blood:
4	chr9:101764776..101767586-chr9:101769172..101770908,2	K562	blood:
5	chr9:101764789..101766455-chr9:101899453..101902305,3	K562	blood:
6	chr9:101764079..101766905-chr9:101863194..101865168,2	MCF-7	breast:
7	chr9:101764776..101766278-chr9:101768248..101770672,2	K562	blood:

Variant related genes	Relation type
ENSG00000106799	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10988510	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs10988521	0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10988530	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11515534	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11515536	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12377855	0.87[CEU][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12379014	0.93[CEU][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12380469	0.87[CEU][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3739799	0.93[CEU][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3780622	0.83[JPT][hapmap]
rs61462449	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022881	0.93[CEU][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7028686	0.86[CEU][hapmap]
rs7032060	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7034847	0.93[CEU][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73503730	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7848837	0.93[CEU][hapmap];0.91[JPT][hapmap];0.98[EUR][1000 genomes]
rs7851787	0.93[CEU][hapmap];0.91[JPT][hapmap];0.98[EUR][1000 genomes]
rs7861925	0.93[CEU][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv6635	chr9:101728257-101773253	Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101760200-101772800	Weak transcription	Aorta	Aorta
2	chr9:101760400-101767400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr9:101761600-101767400	Weak transcription	Colonic Mucosa	Colon
4	chr9:101761600-101768400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:101761600-101770400	Weak transcription	Fetal Intestine Small	intestine
6	chr9:101761600-101814400	Weak transcription	Gastric	stomach
7	chr9:101761800-101765200	Weak transcription	Fetal Stomach	stomach
8	chr9:101761800-101765400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:101761800-101765400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr9:101761800-101765600	Weak transcription	Left Ventricle	heart
11	chr9:101761800-101765800	Weak transcription	Ovary	ovary
12	chr9:101761800-101765800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr9:101761800-101768200	Weak transcription	Spleen	Spleen
14	chr9:101761800-101777800	Weak transcription	Pancreas	Pancrea
15	chr9:101761800-101785200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr9:101762600-101769400	Strong transcription	Fetal Muscle Trunk	muscle
17	chr9:101762800-101765400	Enhancers	Primary T cells from cord blood	blood
18	chr9:101762800-101765400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:101762800-101769000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr9:101762800-101769600	Strong transcription	Stomach Smooth Muscle	stomach
21	chr9:101763000-101765200	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr9:101763000-101765400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:101763000-101765400	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr9:101763000-101765600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:101763000-101765600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:101763000-101765600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr9:101763000-101765800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:101763200-101767200	Weak transcription	Right Ventricle	heart
29	chr9:101763400-101766800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr9:101763600-101765200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr9:101763600-101767600	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr9:101763600-101778000	Weak transcription	HSMMtube	muscle
33	chr9:101763800-101765200	Weak transcription	Brain Hippocampus Middle	brain
34	chr9:101764000-101766000	Enhancers	Placenta	Placenta
35	chr9:101764000-101768200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr9:101764000-101770800	Strong transcription	Fetal Muscle Leg	muscle
37	chr9:101764200-101765200	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr9:101764200-101769400	Strong transcription	Colon Smooth Muscle	Colon
39	chr9:101764200-101772600	Strong transcription	Adipose Nuclei	Adipose
40	chr9:101764200-101775400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr9:101764400-101768200	Weak transcription	Hela-S3	cervix
42	chr9:101764600-101765200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr9:101764600-101766400	Weak transcription	Fetal Thymus	thymus
44	chr9:101764600-101768200	Weak transcription	K562	blood
45	chr9:101764800-101768600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr9:101765000-101765400	Weak transcription	HSMM	muscle

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