Variant report

Variant	rs462487
Chromosome Location	chr6:5139954-5139955
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	chr6:5139257..5141408-chr6:5217631..5219778,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1571564	0.88[JPT][hapmap]
rs175596	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs200859	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs200860	0.88[ASN][1000 genomes]
rs200862	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs200864	0.83[ASN][1000 genomes]
rs200866	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs200867	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs200868	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs200869	0.88[ASN][1000 genomes]
rs200870	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2143693	1.00[JPT][hapmap]
rs2746239	1.00[JPT][hapmap]
rs364857	0.84[CEU][hapmap]
rs373696	0.88[CHB][hapmap]
rs394252	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs399120	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs414986	0.84[ASN][1000 genomes]
rs424006	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs441463	0.83[CEU][hapmap]
rs450176	1.00[JPT][hapmap]
rs452908	0.88[CHB][hapmap]
rs456209	0.84[CEU][hapmap]
rs458743	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs460416	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs462327	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs465481	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs466285	0.88[JPT][hapmap]
rs4960069	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs52401	0.96[ASN][1000 genomes]
rs591481	0.83[CEU][hapmap]
rs6597117	0.86[JPT][hapmap]
rs7752848	1.00[JPT][hapmap]
rs7766717	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription 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	23 gene(s)	inside rSNPs	diseases
6	nsv1017380	chr6:5007870-5152551	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
8	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1017821	chr6:5114609-5213200	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
12	nsv538114	chr6:5114609-5213200	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
13	nsv5179	chr6:5121824-5167027	Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1030254	chr6:5132261-5431585	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
15	nsv1034463	chr6:5137959-5345678	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5129000-5162000	Weak transcription	K562	blood
2	chr6:5130600-5140400	Weak transcription	Gastric	stomach
3	chr6:5130600-5172200	Weak transcription	Lung	lung
4	chr6:5130800-5142400	Weak transcription	Fetal Intestine Small	intestine
5	chr6:5131000-5143000	Weak transcription	Spleen	Spleen
6	chr6:5133200-5141800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:5133400-5143200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:5133400-5143800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:5133400-5144000	Weak transcription	Fetal Brain Male	brain
10	chr6:5133400-5146000	Weak transcription	Psoas Muscle	Psoas
11	chr6:5133400-5151600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:5133600-5143400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:5133600-5143800	Weak transcription	Fetal Stomach	stomach
14	chr6:5133800-5140000	Weak transcription	GM12878-XiMat	blood
15	chr6:5133800-5140600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:5133800-5142400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:5133800-5143000	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:5133800-5143400	Weak transcription	Left Ventricle	heart
19	chr6:5133800-5143600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr6:5133800-5153400	Weak transcription	Right Ventricle	heart
21	chr6:5134200-5144200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr6:5135000-5151000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:5135200-5151800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:5136400-5142400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:5136400-5151000	Weak transcription	NHEK	skin
26	chr6:5136400-5151600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:5137000-5166600	Weak transcription	Primary T cells from cord blood	blood
28	chr6:5139000-5140000	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr6:5139000-5140000	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr6:5139200-5140000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:5139200-5140600	Enhancers	Liver	Liver
32	chr6:5139400-5140000	Enhancers	Fetal Kidney	kidney
33	chr6:5139600-5140000	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr6:5139600-5143200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:5139800-5141600	Enhancers	HepG2	liver
36	chr6:5139800-5141800	Enhancers	Primary B cells from peripheral blood	blood
37	chr6:5139800-5144200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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