Variant report

Variant	rs9490140
Chromosome Location	chr6:121544876-121544877
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:121376435..121377426-chr6:121544734..121545558,2	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12717175	0.95[GIH][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2133988	0.95[GIH][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2133992	0.89[YRI][hapmap]
rs6941235	0.84[YRI][hapmap]
rs7450022	0.84[YRI][hapmap]
rs7775931	0.87[EUR][1000 genomes]
rs9375012	0.84[YRI][hapmap]
rs9398625	0.84[YRI][hapmap]
rs9482122	0.93[CHB][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[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	nsv1023384	chr6:121235867-121683448	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv530527	chr6:121298528-121789855	ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv604572	chr6:121465011-121544876	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv527946	chr6:121544876-121552020	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:121487400-121556000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr6:121509600-121575400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:121516000-121560200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:121528400-121551800	Weak transcription	Psoas Muscle	Psoas
5	chr6:121533000-121566800	Weak transcription	Stomach Mucosa	stomach
6	chr6:121535000-121569200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr6:121536200-121567200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:121536400-121556200	Weak transcription	Primary B cells from cord blood	blood
9	chr6:121536400-121556200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr6:121536600-121545000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:121536600-121556000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:121536600-121556000	Weak transcription	Pancreas	Pancrea
13	chr6:121536600-121556400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:121536600-121556600	Weak transcription	Left Ventricle	heart
15	chr6:121536600-121558400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:121536600-121566000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:121536600-121568200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:121536600-121585400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:121536800-121556000	Weak transcription	Fetal Stomach	stomach
20	chr6:121536800-121556600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:121536800-121565600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr6:121536800-121566000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:121536800-121566000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:121536800-121566000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:121536800-121584400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr6:121537000-121584600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr6:121537200-121556000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr6:121537200-121556200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:121537200-121556200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:121537200-121562400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:121537400-121556200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:121537400-121556600	Weak transcription	Right Ventricle	heart
33	chr6:121537400-121567800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr6:121538200-121565800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:121538200-121567000	Weak transcription	Primary B cells from peripheral blood	blood
36	chr6:121538600-121556000	Weak transcription	Fetal Intestine Small	intestine
37	chr6:121538800-121546200	Weak transcription	Fetal Brain Male	brain
38	chr6:121539200-121567600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr6:121539400-121562200	Weak transcription	Fetal Kidney	kidney
40	chr6:121539400-121563200	Weak transcription	Brain Substantia Nigra	brain
41	chr6:121540200-121555800	Weak transcription	Fetal Intestine Large	intestine
42	chr6:121540400-121555800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:121540400-121556200	Weak transcription	Fetal Lung	lung
44	chr6:121540400-121567800	Weak transcription	Adipose Nuclei	Adipose
45	chr6:121541000-121545200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:121541200-121585000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr6:121541600-121556000	Weak transcription	Primary T cells from cord blood	blood
48	chr6:121542000-121556200	Weak transcription	Ovary	ovary
49	chr6:121544000-121556000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr6:121544400-121556000	Weak transcription	Dnd41	blood

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