Variant report

Variant	rs12530052
Chromosome Location	chr6:80346598-80346599
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:80344145..80347111-chr6:80348069..80350910,2	K562	blood:
2	chr6:80335632..80339568-chr6:80345639..80348961,3	K562	blood:
3	chr6:80339706..80343171-chr6:80343868..80347495,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198478	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1033535	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12525799	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12526427	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs12526644	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527512	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527526	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17505891	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1883879	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34532743	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812155	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812159	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55649340	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55781748	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72901825	1.00[AFR][1000 genomes]
rs72905738	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72905744	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72905757	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[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	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv886302	chr6:80111104-80355973	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1027388	chr6:80113449-80355973	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1018318	chr6:80241029-80465282	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv1032347	chr6:80284809-80694778	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv886304	chr6:80294265-80355973	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80341800-80349800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr6:80341800-80349800	Weak transcription	Lung	lung
3	chr6:80341800-80350200	Weak transcription	Gastric	stomach
4	chr6:80341800-80357600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:80341800-80358600	Weak transcription	HSMM	muscle
6	chr6:80342000-80356000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:80342800-80350200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:80342800-80358600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:80343600-80346600	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr6:80343800-80346800	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr6:80344400-80346800	Enhancers	Stomach Mucosa	stomach
12	chr6:80344400-80349800	Weak transcription	Psoas Muscle	Psoas
13	chr6:80344600-80349600	Weak transcription	Brain Anterior Caudate	brain
14	chr6:80344600-80349600	Weak transcription	K562	blood
15	chr6:80344600-80349800	Weak transcription	Brain Angular Gyrus	brain
16	chr6:80344600-80350000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:80344800-80349800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:80344800-80349800	Weak transcription	Liver	Liver
19	chr6:80344800-80350200	Weak transcription	Fetal Intestine Large	intestine
20	chr6:80344800-80357200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr6:80345000-80349600	Weak transcription	Fetal Brain Male	brain
22	chr6:80345000-80349600	Weak transcription	Fetal Intestine Small	intestine
23	chr6:80345000-80349800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:80345000-80349800	Weak transcription	Brain Hippocampus Middle	brain
25	chr6:80345000-80350200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:80345200-80349800	Weak transcription	Fetal Brain Female	brain
27	chr6:80345200-80350000	Weak transcription	Fetal Kidney	kidney
28	chr6:80345400-80348200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr6:80345400-80349800	Weak transcription	Adipose Nuclei	Adipose
30	chr6:80345400-80349800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr6:80345400-80350000	Weak transcription	Fetal Muscle Leg	muscle
32	chr6:80345400-80350200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:80345400-80350200	Weak transcription	Right Atrium	heart
34	chr6:80345400-80352400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:80345400-80363200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:80345600-80349200	Weak transcription	Small Intestine	intestine
37	chr6:80345600-80349400	Weak transcription	Fetal Lung	lung
38	chr6:80345600-80349800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr6:80345600-80358200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr6:80345600-80359800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr6:80346000-80348600	Weak transcription	HUVEC	blood vessel
42	chr6:80346200-80349000	Weak transcription	Left Ventricle	heart
43	chr6:80346200-80350200	Weak transcription	Esophagus	oesophagus

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