Variant report

Variant	rs16874153
Chromosome Location	chr6:13428397-13428398
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13426005..13428428-chr6:13430205..13432759,2	K562	blood:
2	chr6:13428050..13431790-chr6:13485555..13488109,3	MCF-7	breast:
3	chr6:13426718..13428428-chr6:13429369..13431705,2	K562	blood:

Variant related genes	Relation type
ENSG00000145990	Chromatin interaction
ENSG00000187461	Chromatin interaction
ENSG00000237786	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12527593	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12528480	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs16874132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16874136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16874138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16874139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16874142	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16874145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16874149	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16874152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16874155	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1992387	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs511996	0.82[CEU][hapmap]
rs56676493	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61017983	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6910199	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6914294	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6926083	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6931031	1.00[CHB][hapmap]
rs6936420	0.82[CEU][hapmap]
rs73366922	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73366931	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366933	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366936	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366937	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366941	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366945	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366948	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366949	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366951	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366952	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366960	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366970	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73725822	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7739372	1.00[CHB][hapmap]
rs7740220	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7740298	1.00[CHB][hapmap]
rs7758003	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9370100	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer 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	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS 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 target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1033620	chr6:13419730-13571788	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv462640	chr6:13426539-13519434	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv600994	chr6:13426539-13519434	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13419400-13429800	Enhancers	Fetal Lung	lung
2	chr6:13420200-13430000	Enhancers	Fetal Stomach	stomach
3	chr6:13422000-13428600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:13422200-13432800	Weak transcription	NHDF-Ad	bronchial
5	chr6:13423400-13428800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr6:13423400-13428800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:13423400-13432200	Weak transcription	A549	lung
8	chr6:13423800-13428800	Weak transcription	Fetal Brain Female	brain
9	chr6:13423800-13431400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr6:13423800-13431400	Weak transcription	Brain Germinal Matrix	brain
11	chr6:13423800-13433000	Weak transcription	Pancreas	Pancrea
12	chr6:13424000-13428400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:13424000-13428800	Enhancers	Stomach Smooth Muscle	stomach
14	chr6:13424000-13429000	Weak transcription	Aorta	Aorta
15	chr6:13424000-13429200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:13425200-13429600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:13425200-13430000	Enhancers	Lung	lung
18	chr6:13425200-13430200	Enhancers	Primary B cells from peripheral blood	blood
19	chr6:13425200-13431200	Enhancers	Left Ventricle	heart
20	chr6:13425200-13432200	Enhancers	Right Ventricle	heart
21	chr6:13425400-13428400	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr6:13425400-13430200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:13425800-13428600	Weak transcription	Small Intestine	intestine
24	chr6:13425800-13429800	Enhancers	H1 Cell Line	embryonic stem cell
25	chr6:13426000-13428600	Weak transcription	Colonic Mucosa	Colon
26	chr6:13426000-13429800	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr6:13426000-13430400	Flanking Active TSS	GM12878-XiMat	blood
28	chr6:13426200-13430000	Enhancers	Fetal Thymus	thymus
29	chr6:13426400-13429800	Enhancers	Fetal Heart	heart
30	chr6:13426600-13428400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr6:13426600-13429600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:13426600-13431200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr6:13426800-13428400	Weak transcription	Brain Anterior Caudate	brain
34	chr6:13426800-13428800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:13426800-13429200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr6:13426800-13429400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr6:13426800-13429400	Weak transcription	NHEK	skin
38	chr6:13426800-13431600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr6:13426800-13431600	Weak transcription	NHLF	lung
40	chr6:13426800-13431800	Weak transcription	NH-A	brain
41	chr6:13427000-13428800	Weak transcription	Psoas Muscle	Psoas
42	chr6:13427000-13429400	Weak transcription	Esophagus	oesophagus
43	chr6:13427000-13429600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:13427000-13429600	Weak transcription	HMEC	breast
45	chr6:13427000-13432000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:13427000-13432800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:13427200-13428400	Weak transcription	Spleen	Spleen
48	chr6:13427200-13428800	Weak transcription	Brain Substantia Nigra	brain
49	chr6:13427200-13428800	Weak transcription	Colon Smooth Muscle	Colon
50	chr6:13427400-13428400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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