Variant report

Variant	rs3798593
Chromosome Location	chr6:149341254-149341255
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	chr6:149340644..149342659-chr6:149400805..149403044,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10452661	1.00[CEU][hapmap]
rs11155614	0.92[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11155617	1.00[CEU][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes]
rs17079591	1.00[CEU][hapmap]
rs17081135	1.00[CEU][hapmap]
rs57067744	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57955571	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6900115	1.00[CEU][hapmap]
rs6903661	1.00[CEU][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs7765192	1.00[CEU][hapmap]
rs9373584	1.00[CEU][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes]
rs9373585	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9377189	1.00[CEU][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9386242	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9386243	0.92[JPT][hapmap];1.00[EUR][1000 genomes]
rs9399680	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9404017	1.00[EUR][1000 genomes]
rs9485341	1.00[CEU][hapmap]

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	nsv1032690	chr6:149206106-149398712	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv830842	chr6:149272321-149427340	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149305400-149381400	Weak transcription	Gastric	stomach
2	chr6:149320200-149344800	Weak transcription	Left Ventricle	heart
3	chr6:149321800-149349800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:149323000-149342600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:149327200-149353000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:149327600-149342200	Weak transcription	Dnd41	blood
7	chr6:149333800-149341400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:149333800-149341800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:149333800-149342200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:149334000-149353400	Weak transcription	Spleen	Spleen
11	chr6:149334400-149352800	Weak transcription	HSMMtube	muscle
12	chr6:149336000-149345200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:149336200-149342800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:149336200-149344200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:149336200-149344400	Weak transcription	Fetal Intestine Small	intestine
16	chr6:149336200-149345200	Weak transcription	Right Atrium	heart
17	chr6:149336200-149349800	Weak transcription	Brain Anterior Caudate	brain
18	chr6:149336200-149351400	Weak transcription	Fetal Thymus	thymus
19	chr6:149336200-149353000	Weak transcription	Pancreas	Pancrea
20	chr6:149336200-149353200	Weak transcription	Esophagus	oesophagus
21	chr6:149336200-149358000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:149336400-149347600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr6:149336400-149354000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:149336600-149347400	Weak transcription	Adipose Nuclei	Adipose
25	chr6:149336800-149353200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:149337200-149342600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:149337200-149342800	Weak transcription	Fetal Lung	lung
28	chr6:149337200-149344800	Weak transcription	Fetal Heart	heart
29	chr6:149337200-149347400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:149337200-149353600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr6:149337600-149343600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr6:149337600-149347200	Weak transcription	Osteobl	bone
33	chr6:149337600-149347400	Weak transcription	NH-A	brain
34	chr6:149337600-149352800	Weak transcription	NHLF	lung
35	chr6:149337600-149353000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:149337600-149358000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr6:149337800-149342200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:149338000-149342600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:149338000-149342600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:149338200-149342200	Weak transcription	Fetal Muscle Leg	muscle
41	chr6:149338200-149343800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:149338200-149351800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:149338200-149352400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr6:149338800-149350000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr6:149339200-149342400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr6:149339200-149347000	Weak transcription	Fetal Intestine Large	intestine
47	chr6:149339400-149353200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:149339400-149364600	Weak transcription	Lung	lung
49	chr6:149339600-149342400	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr6:149339600-149342600	Weak transcription	Primary T cells fromperipheralblood	blood

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