Variant report

Variant	rs1000399
Chromosome Location	chr6:15266601-15266602
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15265867..15267617-chr6:15272085..15274902,2	MCF-7	breast:
2	chr6:15265107..15267530-chr6:15269277..15271589,2	MCF-7	breast:
3	chr6:15264451..15267645-chr6:15306826..15309628,3	K562	blood:
4	chr6:15266109..15268889-chr6:15271443..15273014,2	K562	blood:
5	chr6:15265185..15267250-chr6:15444212..15446754,2	K562	blood:
6	chr6:15254326..15257195-chr6:15265565..15267643,2	MCF-7	breast:
7	chr6:15264475..15267087-chr6:15298287..15299928,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11962776	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11965232	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11966818	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11968080	0.87[YRI][hapmap]
rs16876166	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16876169	0.88[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16876182	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17712950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4310061	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57650809	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59272746	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60410720	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6941059	0.89[YRI][hapmap]
rs724971	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73359692	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73359693	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7769631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv538142	chr6:15243960-15404893	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15251200-15279400	Weak transcription	A549	lung
2	chr6:15253200-15269600	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr6:15254200-15269600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:15254800-15269800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:15257800-15270000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr6:15258200-15268600	Enhancers	NHDF-Ad	bronchial
7	chr6:15258800-15267000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:15258800-15268800	Weak transcription	Aorta	Aorta
9	chr6:15258800-15270400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:15261000-15283800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:15261200-15275000	Weak transcription	HMEC	breast
12	chr6:15261600-15268000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:15261600-15270000	Enhancers	Primary T cells fromperipheralblood	blood
14	chr6:15261600-15270600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:15262400-15268000	Enhancers	NHLF	lung
16	chr6:15262400-15270200	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr6:15262600-15269600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr6:15262800-15270000	Enhancers	Fetal Thymus	thymus
19	chr6:15262800-15270000	Enhancers	Spleen	Spleen
20	chr6:15262800-15270200	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr6:15262800-15271200	Enhancers	Primary B cells from peripheral blood	blood
22	chr6:15263000-15267000	Enhancers	Thymus	Thymus
23	chr6:15263000-15267600	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr6:15263000-15269000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:15263000-15269400	Enhancers	Psoas Muscle	Psoas
26	chr6:15263000-15269600	Enhancers	Right Ventricle	heart
27	chr6:15263000-15270200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr6:15263000-15271400	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr6:15263200-15267200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr6:15263200-15268400	Enhancers	Adipose Nuclei	Adipose
31	chr6:15263200-15269800	Enhancers	Left Ventricle	heart
32	chr6:15263200-15270000	Enhancers	Fetal Muscle Leg	muscle
33	chr6:15263200-15270200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:15264000-15267200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:15264000-15269400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:15264000-15269800	Enhancers	Gastric	stomach
37	chr6:15264200-15267600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr6:15264200-15268800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr6:15264200-15269400	Enhancers	NH-A	brain
40	chr6:15264200-15269800	Enhancers	Fetal Lung	lung
41	chr6:15264200-15270000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr6:15264200-15270000	Enhancers	Fetal Stomach	stomach
43	chr6:15264200-15270200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr6:15264200-15270200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr6:15264200-15270200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr6:15264200-15270200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:15264200-15270200	Enhancers	Fetal Heart	heart
48	chr6:15264200-15270600	Enhancers	Ovary	ovary
49	chr6:15264200-15272800	Enhancers	Brain Angular Gyrus	brain
50	chr6:15264400-15267600	Flanking Active TSS	GM12878-XiMat	blood

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