Variant report

Variant	rs12061601
Chromosome Location	chr1:169070450-169070451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169067096..169070478-chr1:169071882..169077331,7	K562	blood:
2	chr1:169064466..169066505-chr1:169069243..169071923,2	MCF-7	breast:
3	chr1:169053133..169065213-chr1:169070028..169077898,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237707	Chromatin interaction
ENSG00000143153	Chromatin interaction
ENSG00000203601	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12079856	0.98[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12751593	0.90[EUR][1000 genomes]
rs1320976	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1320977	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1534984	0.91[EUR][1000 genomes]
rs1892092	0.93[EUR][1000 genomes]
rs1892093	0.92[EUR][1000 genomes]
rs28362572	0.93[EUR][1000 genomes]
rs4656647	0.92[EUR][1000 genomes]
rs59732929	0.98[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs6672876	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv831858	chr1:169022383-169179068	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
QT interval	24952745	GWAS catalog

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169064800-169071600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:169067600-169071800	Enhancers	Brain Angular Gyrus	brain
3	chr1:169067800-169071200	Enhancers	Stomach Mucosa	stomach
4	chr1:169067800-169071600	Enhancers	Brain Substantia Nigra	brain
5	chr1:169068000-169070600	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr1:169068000-169070800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:169068000-169074600	Enhancers	Fetal Heart	heart
8	chr1:169068200-169071200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:169068400-169071600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:169068800-169072400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:169068800-169074600	Enhancers	Fetal Intestine Large	intestine
12	chr1:169068800-169074600	Enhancers	Fetal Intestine Small	intestine
13	chr1:169069000-169072400	Weak transcription	Fetal Kidney	kidney
14	chr1:169069000-169072800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:169069200-169074400	Enhancers	HepG2	liver
16	chr1:169069400-169070800	Enhancers	Liver	Liver
17	chr1:169069400-169071000	Enhancers	Colonic Mucosa	Colon
18	chr1:169069400-169071400	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr1:169069400-169071600	Enhancers	Brain Cingulate Gyrus	brain
20	chr1:169069400-169071600	Enhancers	Brain Hippocampus Middle	brain
21	chr1:169069600-169070600	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr1:169069600-169071600	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr1:169069600-169071800	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr1:169069800-169071200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:169069800-169071600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:169069800-169071800	Weak transcription	Right Ventricle	heart
27	chr1:169070000-169070600	Weak transcription	Brain Anterior Caudate	brain
28	chr1:169070000-169070800	Weak transcription	Left Ventricle	heart
29	chr1:169070000-169071000	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr1:169070000-169071200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:169070000-169071200	Weak transcription	Esophagus	oesophagus
32	chr1:169070000-169071600	Weak transcription	Right Atrium	heart
33	chr1:169070000-169071600	Weak transcription	Small Intestine	intestine
34	chr1:169070000-169073800	Weak transcription	Gastric	stomach
35	chr1:169070200-169071800	Weak transcription	Pancreas	Pancrea
36	chr1:169070400-169071800	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr1:169070400-169072800	Enhancers	Placenta Amnion	Placenta Amnion
38	chr1:169070400-169073000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:169070400-169073000	Enhancers	Cortex derived primary cultured neurospheres	brain

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