Variant report

Variant	rs393628
Chromosome Location	chr6:5109119-5109120
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5095410..5098025-chr6:5107266..5109190,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs200844	0.80[AMR][1000 genomes]
rs200860	0.86[AMR][1000 genomes]
rs200866	0.82[CEU][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs200869	0.86[AMR][1000 genomes]
rs374117	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs375064	0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs379508	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs379511	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs381472	0.82[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs388597	0.82[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs391176	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs393300	0.82[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs393332	0.82[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs411483	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs414986	0.80[AMR][1000 genomes]
rs424006	0.82[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs434706	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs457206	0.87[ASN][1000 genomes]
rs457759	0.88[CHD][hapmap]
rs458108	0.82[CEU][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs458283	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs458743	0.82[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs459200	0.84[ASN][1000 genomes]
rs460440	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs461465	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs462327	0.82[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs465453	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs465481	0.82[CEU][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs466285	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs466906	1.00[LWK][hapmap]
rs620360	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv1017373	chr6:5066785-5128943	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv538112	chr6:5066785-5128943	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5095800-5114200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:5096000-5112200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:5097600-5112800	Weak transcription	K562	blood
4	chr6:5098600-5117000	Weak transcription	Fetal Brain Female	brain
5	chr6:5099000-5130000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:5101800-5132200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr6:5102800-5110400	Weak transcription	Primary T cells from cord blood	blood
8	chr6:5102800-5111600	Weak transcription	Thymus	Thymus
9	chr6:5103000-5113000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:5103200-5113600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:5103200-5114000	Weak transcription	Dnd41	blood
12	chr6:5103200-5132800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr6:5103400-5110600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr6:5103800-5112200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:5103800-5112400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:5104200-5112000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:5104200-5112200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:5105000-5109400	Weak transcription	NHEK	skin
19	chr6:5105000-5113200	Strong transcription	HepG2	liver
20	chr6:5105200-5115800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:5105200-5131400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:5105800-5125600	Weak transcription	Ovary	ovary
23	chr6:5105800-5128200	Weak transcription	Primary B cells from cord blood	blood
24	chr6:5106800-5111800	Strong transcription	Fetal Stomach	stomach
25	chr6:5107000-5110800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr6:5107200-5109400	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr6:5107200-5109600	Weak transcription	Gastric	stomach
28	chr6:5107200-5112600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr6:5107400-5109400	Genic enhancers	Fetal Muscle Leg	muscle
30	chr6:5107400-5110400	Strong transcription	Adipose Nuclei	Adipose
31	chr6:5107600-5109800	Enhancers	Fetal Intestine Large	intestine
32	chr6:5107600-5111000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr6:5107600-5111800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:5107800-5111600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:5107800-5112200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr6:5107800-5132000	Weak transcription	Pancreas	Pancrea
37	chr6:5108000-5110600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr6:5108000-5113600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr6:5108200-5110000	Enhancers	Fetal Intestine Small	intestine
40	chr6:5108200-5112200	Weak transcription	Aorta	Aorta
41	chr6:5108200-5112800	Strong transcription	Spleen	Spleen
42	chr6:5108400-5112400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:5108600-5109200	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr6:5108600-5109200	Enhancers	HSMMtube	muscle
45	chr6:5108600-5110800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:5108600-5111800	Weak transcription	Fetal Thymus	thymus
47	chr6:5108600-5112200	Weak transcription	Fetal Lung	lung
48	chr6:5108800-5109200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:5108800-5109200	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr6:5108800-5109200	Genic enhancers	Fetal Muscle Trunk	muscle

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