Variant report

Variant	rs6427580
Chromosome Location	chr1:161236456-161236457
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	chr1:161228430..161230750-chr1:161235534..161238135,2	MCF-7	breast:
2	chr1:161227688..161230234-chr1:161234768..161237380,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248485	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2501871	0.85[ASN][1000 genomes]
rs2501875	0.85[ASN][1000 genomes]
rs2502811	0.87[ASN][1000 genomes]
rs6427581	0.86[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs6657761	0.85[ASN][1000 genomes]
rs6682220	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv432986	chr1:161221133-161673682	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv520253	chr1:161234623-161237892	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6427580	ASH1L	cis	parietal	SCAN
rs6427580	DCAF8	cis	parietal	SCAN
rs6427580	C1orf192	cis	parietal	SCAN
rs6427580	PPOX	cis	parietal	SCAN
rs6427580	FCRL4	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161232000-161236600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:161232600-161237000	Weak transcription	GM12878-XiMat	blood
3	chr1:161233400-161237000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:161234800-161237600	Enhancers	Ovary	ovary
5	chr1:161235000-161237400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:161235200-161237400	Enhancers	Rectal Smooth Muscle	rectum
7	chr1:161235200-161238000	Enhancers	Fetal Stomach	stomach
8	chr1:161235400-161237200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:161235600-161237200	Weak transcription	Placenta	Placenta
10	chr1:161235800-161236600	Enhancers	HSMM	muscle
11	chr1:161235800-161236800	Bivalent Enhancer	Osteobl	bone
12	chr1:161235800-161237000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr1:161235800-161237200	Enhancers	Brain Anterior Caudate	brain
14	chr1:161235800-161237200	Enhancers	HSMMtube	muscle
15	chr1:161235800-161237400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr1:161235800-161237400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:161235800-161237400	Enhancers	A549	lung
18	chr1:161235800-161237600	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr1:161235800-161237600	Enhancers	Fetal Muscle Leg	muscle
20	chr1:161236000-161236600	Enhancers	Muscle Satellite Cultured Cells	--
21	chr1:161236000-161236800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:161236000-161236800	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr1:161236000-161237200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:161236000-161237200	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr1:161236000-161237200	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr1:161236000-161237400	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr1:161236000-161237400	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr1:161236000-161237400	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr1:161236000-161237400	Enhancers	Pancreas	Pancrea
30	chr1:161236200-161236800	Enhancers	Right Ventricle	heart
31	chr1:161236200-161237200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr1:161236200-161237200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr1:161236200-161237400	Enhancers	Left Ventricle	heart
34	chr1:161236400-161236600	Enhancers	Fetal Heart	heart
35	chr1:161236400-161236800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:161236400-161237200	Enhancers	Colon Smooth Muscle	Colon

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