Variant report

Variant	rs3994138
Chromosome Location	chr9:100466044-100466045
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100465773..100467417-chr9:100473375..100476124,2	MCF-7	breast:
2	chr9:100457791..100462084-chr9:100462112..100466505,5	K562	blood:
3	chr9:100462976..100466831-chr9:100467484..100471759,4	K562	blood:
4	chr9:100456256..100459810-chr9:100463870..100468057,7	MCF-7	breast:
5	chr9:100465031..100468402-chr9:100745252..100748120,3	MCF-7	breast:
6	chr9:100464367..100467056-chr9:100650913..100653289,2	K562	blood:
7	chr9:100458037..100462084-chr9:100463856..100467658,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136936	Chromatin interaction
ENSG00000214417	Chromatin interaction
ENSG00000136938	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10983035	0.83[JPT][hapmap]
rs1355599	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2805767	0.87[JPT][hapmap]
rs2805777	0.87[JPT][hapmap]
rs2805827	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2808672	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2808679	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2808680	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3176689	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1043753	chr9:100458109-100599265	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv972792	chr9:100460351-100466365	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100459800-100466400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:100460400-100467000	Weak transcription	Esophagus	oesophagus
3	chr9:100460400-100467800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr9:100461400-100467800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr9:100461600-100467200	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr9:100462400-100472800	Weak transcription	Brain Substantia Nigra	brain
7	chr9:100465000-100466600	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr9:100465000-100466800	Enhancers	Fetal Intestine Small	intestine
9	chr9:100465200-100466600	Enhancers	Liver	Liver
10	chr9:100465200-100467000	Enhancers	GM12878-XiMat	blood
11	chr9:100465200-100467200	Enhancers	Placenta Amnion	Placenta Amnion
12	chr9:100465400-100466200	Enhancers	HSMMtube	muscle
13	chr9:100465400-100466600	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr9:100465400-100466800	Flanking Active TSS	A549	lung
15	chr9:100465400-100467200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:100465400-100467200	Enhancers	Fetal Intestine Large	intestine
17	chr9:100465400-100469000	Enhancers	HMEC	breast
18	chr9:100465600-100466800	Flanking Active TSS	Hela-S3	cervix
19	chr9:100465600-100466800	Enhancers	NHDF-Ad	bronchial
20	chr9:100465600-100467000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr9:100465600-100467200	Enhancers	Pancreas	Pancrea
22	chr9:100465600-100468600	Enhancers	HUVEC	blood vessel
23	chr9:100465600-100468800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr9:100465600-100468800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr9:100465800-100466200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:100465800-100466200	Enhancers	Fetal Kidney	kidney
27	chr9:100465800-100466600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:100465800-100466600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:100465800-100466600	Flanking Active TSS	HepG2	liver
30	chr9:100465800-100466600	Flanking Active TSS	HSMM	muscle
31	chr9:100465800-100466800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr9:100465800-100466800	Enhancers	NHLF	lung
33	chr9:100465800-100467000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr9:100465800-100467000	Enhancers	Stomach Mucosa	stomach
35	chr9:100465800-100467000	Flanking Active TSS	NH-A	brain
36	chr9:100465800-100467000	Flanking Active TSS	NHEK	skin
37	chr9:100465800-100467400	Enhancers	Rectal Smooth Muscle	rectum
38	chr9:100466000-100466200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr9:100466000-100466200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr9:100466000-100466200	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr9:100466000-100466400	Flanking Active TSS	Osteobl	bone
42	chr9:100466000-100466600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:100466000-100466600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr9:100466000-100466800	Enhancers	K562	blood
45	chr9:100466000-100467200	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr9:100466000-100467200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr9:100466000-100467400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:100466000-100467800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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