Variant report

Variant	rs6427588
Chromosome Location	chr1:161270716-161270717
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:161269161..161270798-chr1:161282887..161284845,2	MCF-7	breast:
2	chr1:161269370..161272593-chr1:161272649..161275995,5	K562	blood:
3	chr1:161263327..161265806-chr1:161269282..161270908,2	K562	blood:

Variant related genes	Relation type
ENSG00000143252	Chromatin interaction
ENSG00000158887	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10081966	0.83[CHB][hapmap]
rs11265582	0.80[ASN][1000 genomes]
rs11265583	0.84[ASN][1000 genomes]
rs12023218	0.93[ASN][1000 genomes]
rs12088460	0.80[ASN][1000 genomes]
rs12094828	0.84[ASN][1000 genomes]
rs12727003	0.84[ASN][1000 genomes]
rs4075971	0.84[ASN][1000 genomes]
rs4255401	0.80[ASN][1000 genomes]
rs4436408	0.90[CHB][hapmap];0.82[CHD][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs4582821	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs4636484	0.82[ASN][1000 genomes]
rs4657009	0.80[ASN][1000 genomes]
rs4657013	0.89[CHB][hapmap];0.87[ASN][1000 genomes]
rs4657015	0.80[CHB][hapmap]
rs4657016	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6427584	0.80[ASN][1000 genomes]
rs7545977	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9651049	0.90[CHB][hapmap];0.85[CHD][hapmap];0.85[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	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	nsv525443	chr1:161263380-161274311	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv517826	chr1:161263380-161277601	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6427588	C1orf192	cis	parietal	SCAN
rs6427588	ETV3L	cis	parietal	SCAN
rs6427588	ISG20L2	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161250400-161274200	Weak transcription	Fetal Stomach	stomach
2	chr1:161252400-161274800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:161255200-161274800	Weak transcription	Lung	lung
4	chr1:161255600-161274600	Weak transcription	Adipose Nuclei	Adipose
5	chr1:161256400-161272800	Weak transcription	Primary T cells from cord blood	blood
6	chr1:161261000-161272800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:161261400-161273200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:161261400-161273800	Weak transcription	Fetal Intestine Small	intestine
9	chr1:161261600-161274200	Weak transcription	Fetal Intestine Large	intestine
10	chr1:161263200-161274600	Weak transcription	Placenta	Placenta
11	chr1:161265800-161273600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:161266200-161273800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr1:161267000-161273200	Weak transcription	Primary B cells from cord blood	blood
14	chr1:161267600-161273800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr1:161268200-161272600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:161268200-161273800	Weak transcription	GM12878-XiMat	blood
17	chr1:161268400-161272000	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:161268400-161272800	Weak transcription	Primary B cells from peripheral blood	blood
19	chr1:161269000-161271200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:161269000-161272800	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr1:161269000-161273200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:161269400-161272600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr1:161269400-161273200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:161269400-161273400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr1:161269400-161273800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:161269400-161274000	Weak transcription	K562	blood
27	chr1:161269400-161274200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:161269400-161274200	Weak transcription	Brain Angular Gyrus	brain
29	chr1:161269400-161274400	Weak transcription	Small Intestine	intestine
30	chr1:161269600-161271200	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr1:161269600-161272000	Weak transcription	HUVEC	blood vessel
32	chr1:161269600-161273200	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr1:161269600-161273200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:161269800-161272800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:161269800-161273000	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr1:161269800-161274800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:161269800-161274800	Weak transcription	Pancreas	Pancrea
38	chr1:161270000-161275000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:161270400-161270800	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr1:161270400-161270800	Enhancers	H9 Cell Line	embryonic stem cell
41	chr1:161270400-161270800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:161270400-161270800	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr1:161270400-161271200	Enhancers	Fetal Heart	heart
44	chr1:161270600-161273400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:161270600-161273800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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