Variant report

Variant	rs573109
Chromosome Location	chr6:13373409-13373410
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	chr6:13371659..13373968-chr6:13405951..13408760,2	K562	blood:
2	chr6:13370869..13372385-chr6:13372933..13375526,2	K562	blood:

Variant related genes	Relation type
ENSG00000145990	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10807431	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10807432	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10948650	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12153966	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2439536	0.93[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2496139	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2496160	0.92[CEU][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2496161	0.92[CEU][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2496162	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs2496173	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28813108	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4711978	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs474159	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs476904	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs489396	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs491278	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs492433	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs501987	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs510932	1.00[CEU][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs516003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs517803	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs524118	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs531256	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs548119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs552655	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs553671	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs553948	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs560396	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs564174	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs570315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs575709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579028	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7760579	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7770078	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs821276	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs821277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9357708	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9367440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13355600-13383400	Weak transcription	A549	lung
2	chr6:13356200-13373600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:13356200-13378200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:13361600-13378200	Weak transcription	Fetal Thymus	thymus
5	chr6:13365000-13377800	Weak transcription	Primary B cells from cord blood	blood
6	chr6:13365400-13379800	Weak transcription	Primary T cells from cord blood	blood
7	chr6:13365600-13378000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:13365800-13373800	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr6:13365800-13373800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:13365800-13373800	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr6:13365800-13377600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr6:13365800-13378800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:13365800-13378800	Weak transcription	Gastric	stomach
14	chr6:13365800-13379400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:13365800-13379600	Weak transcription	Brain Germinal Matrix	brain
16	chr6:13365800-13380600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr6:13365800-13385400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:13366000-13374600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:13366000-13378200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr6:13366000-13378200	Weak transcription	Colonic Mucosa	Colon
21	chr6:13366000-13378600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:13366000-13380600	Weak transcription	Ovary	ovary
23	chr6:13366000-13382800	Weak transcription	Liver	Liver
24	chr6:13366000-13386800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:13367600-13374400	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr6:13368000-13404600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr6:13368200-13381000	Weak transcription	NH-A	brain
28	chr6:13368400-13373800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr6:13368400-13375800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:13368400-13386600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:13368600-13373600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:13368600-13375600	Weak transcription	Esophagus	oesophagus
33	chr6:13368600-13377600	Weak transcription	Aorta	Aorta
34	chr6:13368800-13373800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr6:13368800-13375400	Weak transcription	Psoas Muscle	Psoas
36	chr6:13369600-13373800	Weak transcription	NHLF	lung
37	chr6:13370600-13374400	Enhancers	Fetal Heart	heart
38	chr6:13371000-13374400	Enhancers	Adipose Nuclei	Adipose
39	chr6:13371200-13373600	Enhancers	Placenta	Placenta
40	chr6:13371600-13373600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr6:13371600-13374400	Enhancers	Stomach Smooth Muscle	stomach
42	chr6:13371600-13375400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:13371800-13375200	Weak transcription	NHEK	skin
44	chr6:13371800-13375400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:13371800-13375600	Weak transcription	HMEC	breast
46	chr6:13372000-13373600	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr6:13372200-13375400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:13372200-13380600	Weak transcription	Lung	lung
49	chr6:13372400-13381000	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr6:13372800-13374000	Weak transcription	Brain Substantia Nigra	brain

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