Variant report

Variant	rs59594955
Chromosome Location	chr6:38411122-38411123
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38410346..38413041-chr6:38421338..38423278,2	MCF-7	breast:
2	chr6:38409873..38411784-chr6:38412186..38413893,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11964058	0.97[AFR][1000 genomes]
rs12200371	1.00[ASN][1000 genomes]
rs12528414	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12528840	0.90[AFR][1000 genomes]
rs16890682	0.84[EUR][1000 genomes]
rs16890715	0.95[AFR][1000 genomes]
rs28587676	0.92[EUR][1000 genomes]
rs35978718	1.00[ASN][1000 genomes]
rs4236059	0.95[ASN][1000 genomes]
rs4316001	0.81[ASN][1000 genomes]
rs4400204	0.92[EUR][1000 genomes]
rs60581943	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61088409	0.86[ASN][1000 genomes]
rs6912811	0.86[ASN][1000 genomes]
rs6941817	0.90[AFR][1000 genomes]
rs7764900	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9470889	0.86[ASN][1000 genomes]
rs9688895	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9689697	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1032358	chr6:38323745-38415855	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1022724	chr6:38332368-38454527	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv602958	chr6:38362024-38446634	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1030889	chr6:38374812-38450432	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 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	chr6:38376800-38411400	Weak transcription	Primary T cells from cord blood	blood
2	chr6:38396400-38449800	Weak transcription	Primary B cells from cord blood	blood
3	chr6:38398800-38413800	Weak transcription	Aorta	Aorta
4	chr6:38402600-38411200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:38404800-38413800	Weak transcription	Small Intestine	intestine
6	chr6:38405000-38411200	Weak transcription	HSMM	muscle
7	chr6:38405200-38413800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:38405200-38420800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:38405400-38413000	Weak transcription	Fetal Heart	heart
10	chr6:38408200-38419200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr6:38408800-38412000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr6:38409200-38413800	Weak transcription	Ovary	ovary
13	chr6:38409800-38411600	Weak transcription	Psoas Muscle	Psoas
14	chr6:38410000-38412400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr6:38410400-38412000	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr6:38410600-38412000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr6:38410800-38412000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr6:38410800-38412000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:38410800-38412000	Enhancers	Brain Hippocampus Middle	brain
20	chr6:38410800-38412400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:38410800-38412600	Enhancers	Primary hematopoietic stem cells	blood
22	chr6:38411000-38411400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr6:38411000-38411400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:38411000-38411600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:38411000-38411600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:38411000-38411600	Enhancers	Brain Cingulate Gyrus	brain
27	chr6:38411000-38411600	Enhancers	Brain Germinal Matrix	brain
28	chr6:38411000-38411800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:38411000-38411800	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr6:38411000-38411800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:38411000-38411800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr6:38411000-38411800	Enhancers	Brain Angular Gyrus	brain
33	chr6:38411000-38411800	Enhancers	HSMMtube	muscle
34	chr6:38411000-38412000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr6:38411000-38412000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:38411000-38412000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:38411000-38412000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:38411000-38412000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:38411000-38412000	Enhancers	Adipose Nuclei	Adipose
40	chr6:38411000-38412000	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr6:38411000-38412000	Enhancers	Brain Substantia Nigra	brain
42	chr6:38411000-38412000	Enhancers	GM12878-XiMat	blood
43	chr6:38411000-38412000	Enhancers	NHEK	skin
44	chr6:38411000-38412200	Enhancers	Brain Anterior Caudate	brain
45	chr6:38411000-38412200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:38411000-38412200	Enhancers	Sigmoid Colon	Sigmoid Colon

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