Variant report

Variant	rs9399496
Chromosome Location	chr6:145066167-145066168
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	chr6:145055209..145057241-chr6:145065658..145067818,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11155374	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12661505	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12663956	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12665635	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4143940	0.98[ASN][1000 genomes]
rs4143941	1.00[ASN][1000 genomes]
rs4499950	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9321995	0.85[JPT][hapmap]
rs9373426	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9376847	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9376848	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9376849	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9376850	0.96[ASN][1000 genomes]
rs9376851	0.96[ASN][1000 genomes]
rs9376856	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9376861	0.86[JPT][hapmap]
rs9386083	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9390204	1.00[ASN][1000 genomes]
rs9390207	1.00[ASN][1000 genomes]
rs9390209	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9390210	1.00[ASN][1000 genomes]
rs9390213	0.96[ASN][1000 genomes]
rs9390214	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9390216	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9390225	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9390227	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9390237	0.86[JPT][hapmap]
rs9399497	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9399498	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9399499	1.00[ASN][1000 genomes]
rs9399500	0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9403597	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9403598	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9403599	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9403600	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9403601	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9403607	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9403612	0.89[JPT][hapmap]
rs9403613	0.98[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	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1032838	chr6:144978504-145110121	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830833	chr6:145001310-145201143	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1021098	chr6:145017386-145106441	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145011800-145090200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr6:145011800-145096600	Weak transcription	Thymus	Thymus
3	chr6:145018400-145069000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:145024000-145087200	Weak transcription	Psoas Muscle	Psoas
5	chr6:145040000-145094600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:145040000-145114600	Weak transcription	NHLF	lung
7	chr6:145044200-145069400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr6:145046000-145122200	Weak transcription	Colonic Mucosa	Colon
9	chr6:145047200-145077400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:145047600-145075000	Weak transcription	Gastric	stomach
11	chr6:145047600-145083400	Weak transcription	Right Ventricle	heart
12	chr6:145047600-145096600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:145047600-145115000	Weak transcription	Esophagus	oesophagus
14	chr6:145047600-145115000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:145047800-145079600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:145047800-145079600	Weak transcription	NHEK	skin
17	chr6:145049400-145098400	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr6:145049600-145088800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:145051000-145069200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:145051800-145072200	Weak transcription	Osteobl	bone
21	chr6:145053000-145070000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:145053000-145072800	Weak transcription	NHDF-Ad	bronchial
23	chr6:145053000-145079800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:145053200-145073800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr6:145053400-145069400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr6:145054000-145068400	Weak transcription	NH-A	brain
27	chr6:145054000-145072600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr6:145054000-145095600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr6:145054200-145069200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr6:145054200-145069400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:145054200-145072600	Weak transcription	HUVEC	blood vessel
32	chr6:145054200-145072800	Weak transcription	Ovary	ovary
33	chr6:145054200-145093400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr6:145054400-145069600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr6:145054400-145100000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr6:145055000-145068400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:145055000-145069400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr6:145055400-145069400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:145055400-145069400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:145056000-145069400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr6:145056000-145072600	Weak transcription	GM12878-XiMat	blood
42	chr6:145056200-145069600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:145056400-145072600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr6:145056400-145072800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr6:145056600-145067800	Weak transcription	HSMMtube	muscle
46	chr6:145056600-145068400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr6:145056600-145072800	Weak transcription	Fetal Muscle Leg	muscle
48	chr6:145056600-145078600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr6:145058000-145068800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr6:145058400-145066600	Weak transcription	HSMM	muscle

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