Variant report

Variant	rs1223397
Chromosome Location	chr6:13270945-13270946
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:13270057-13271195	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:13268970..13278598-chr6:13326296..13332818,15	K562	blood:
2	chr6:13258559..13263124-chr6:13265994..13271116,8	K562	blood:
3	chr6:13259737..13263124-chr6:13265994..13271257,6	K562	blood:

Variant related genes	Relation type
PHACTR1	TF binding region
ENSG00000145979	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1223399	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1223400	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1223401	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1223402	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1223403	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1232392	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13191897	0.85[CEU][hapmap]
rs13205692	0.80[EUR][1000 genomes]
rs17700321	0.92[CEU][hapmap];0.91[MEX][hapmap];0.84[EUR][1000 genomes]
rs17767967	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs202018	0.81[JPT][hapmap]
rs202019	0.81[JPT][hapmap]
rs202021	0.81[JPT][hapmap]
rs202023	0.81[JPT][hapmap]
rs20499	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs20500	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2439534	0.81[JPT][hapmap]
rs2439537	0.81[JPT][hapmap]
rs2439539	0.81[JPT][hapmap]
rs2439541	0.87[JPT][hapmap]
rs2439542	0.81[JPT][hapmap]
rs2439545	0.81[JPT][hapmap]
rs2439548	0.81[JPT][hapmap]
rs2458310	0.81[JPT][hapmap]
rs2458311	0.81[JPT][hapmap]
rs2458312	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs2458313	0.84[CEU][hapmap]
rs2458314	0.81[JPT][hapmap]
rs2496140	0.81[JPT][hapmap]
rs2496142	0.81[JPT][hapmap]
rs2496144	0.81[JPT][hapmap]
rs2496145	0.81[JPT][hapmap]
rs2496147	0.81[JPT][hapmap]
rs2496148	0.81[JPT][hapmap]
rs2496156	0.81[JPT][hapmap]
rs2496157	0.81[JPT][hapmap]
rs34505804	0.80[EUR][1000 genomes]
rs35511719	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35549743	0.80[EUR][1000 genomes]
rs3734878	0.92[CEU][hapmap];0.91[MEX][hapmap];0.80[EUR][1000 genomes]
rs3817737	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3817738	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3817741	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3817742	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs402705	0.81[JPT][hapmap]
rs449727	0.81[JPT][hapmap]
rs453877	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs617580	0.88[JPT][hapmap]
rs641758	0.81[JPT][hapmap]
rs68050381	0.89[ASN][1000 genomes]
rs9357660	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9381884	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9395602	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[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

Variant related diseases (count:1)

Disease	PMID	Source
Blood pressure	22763476	GWAS catalog

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13249200-13272200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr6:13249800-13287000	Weak transcription	Fetal Brain Male	brain
3	chr6:13256600-13272200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:13256600-13273200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:13256600-13278200	Weak transcription	Pancreas	Pancrea
6	chr6:13258800-13272200	Weak transcription	Left Ventricle	heart
7	chr6:13261400-13272200	Weak transcription	Brain Angular Gyrus	brain
8	chr6:13261400-13272200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:13261400-13273000	Weak transcription	Adipose Nuclei	Adipose
10	chr6:13261600-13272200	Weak transcription	Brain Hippocampus Middle	brain
11	chr6:13262600-13272400	Enhancers	Primary B cells from peripheral blood	blood
12	chr6:13262600-13272800	Weak transcription	Primary T cells from cord blood	blood
13	chr6:13263400-13272400	Weak transcription	Spleen	Spleen
14	chr6:13264600-13272200	Weak transcription	Fetal Muscle Leg	muscle
15	chr6:13267000-13274200	Weak transcription	Gastric	stomach
16	chr6:13267200-13272000	Enhancers	Primary B cells from cord blood	blood
17	chr6:13267400-13272000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:13267400-13272200	Weak transcription	Brain Germinal Matrix	brain
19	chr6:13267400-13272200	Weak transcription	Fetal Stomach	stomach
20	chr6:13267400-13280400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:13267400-13283600	Weak transcription	Fetal Brain Female	brain
22	chr6:13267800-13272000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr6:13267800-13272200	Weak transcription	Brain Anterior Caudate	brain
24	chr6:13268000-13278800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:13268000-13283600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:13268400-13272200	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr6:13268800-13271000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:13269000-13271200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:13269000-13272600	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr6:13269200-13282000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:13269400-13272200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:13269400-13274200	Weak transcription	Aorta	Aorta
33	chr6:13269400-13275400	Weak transcription	Right Ventricle	heart
34	chr6:13269400-13284800	Weak transcription	Right Atrium	heart
35	chr6:13269600-13272000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:13269600-13272600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:13269600-13273000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr6:13269600-13273000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:13269600-13273200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr6:13269600-13275600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:13269600-13286600	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr6:13269600-13286600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr6:13269800-13271200	Enhancers	K562	blood
44	chr6:13270200-13272000	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr6:13270200-13272400	Weak transcription	Placenta	Placenta
46	chr6:13270200-13272800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:13270200-13273800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr6:13270200-13291600	Weak transcription	HSMM	muscle
49	chr6:13270400-13271000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr6:13270400-13282000	Weak transcription	Ovary	ovary

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