Variant report

Variant	rs12130489
Chromosome Location	chr1:180089733-180089734
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	chr1:180088093..180090445-chr1:180090523..180092506,2	MCF-7	breast:
2	chr1:180081238..180084639-chr1:180085491..180090263,5	K562	blood:

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10442618	0.87[EUR][1000 genomes]
rs10494524	1.00[CEU][hapmap]
rs12116940	0.84[EUR][1000 genomes]
rs12118265	0.81[AMR][1000 genomes]
rs12118985	0.93[EUR][1000 genomes]
rs12119130	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12120418	0.88[EUR][1000 genomes]
rs12121834	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12121845	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12123139	0.86[EUR][1000 genomes]
rs12123560	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap]
rs12124265	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12125556	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12125592	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12125693	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12125893	0.87[EUR][1000 genomes]
rs12126967	0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs12127784	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12129115	0.81[EUR][1000 genomes]
rs12130397	0.83[EUR][1000 genomes]
rs12130479	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12131200	0.83[TSI][hapmap]
rs12132694	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap]
rs12134536	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12135751	1.00[CEU][hapmap]
rs12135828	0.83[EUR][1000 genomes]
rs12138201	0.93[EUR][1000 genomes]
rs12138429	0.84[EUR][1000 genomes]
rs12138974	0.92[EUR][1000 genomes]
rs12139323	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap]
rs12139412	1.00[CEU][hapmap]
rs12139761	0.90[EUR][1000 genomes]
rs12140235	0.96[EUR][1000 genomes]
rs12140589	0.83[EUR][1000 genomes]
rs12140868	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12141817	1.00[CEU][hapmap]
rs12144328	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12144346	0.83[TSI][hapmap]
rs12144352	0.83[TSI][hapmap]
rs12145411	1.00[CEU][hapmap]
rs12184265	0.81[EUR][1000 genomes]
rs12184270	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs16843139	1.00[CEU][hapmap];0.88[YRI][hapmap];0.93[EUR][1000 genomes]
rs16855014	0.82[CHD][hapmap]
rs16855019	1.00[CEU][hapmap]
rs16855021	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap]
rs16855022	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap]
rs16855025	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap]
rs16855048	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap]
rs16855049	0.91[CEU][hapmap];0.88[YRI][hapmap]
rs16855070	0.83[EUR][1000 genomes]
rs16855107	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs16855110	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap];0.87[EUR][1000 genomes]
rs16855125	1.00[CEU][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes]
rs16855130	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs16855268	1.00[CEU][hapmap];0.88[YRI][hapmap];0.92[EUR][1000 genomes]
rs16855270	0.93[EUR][1000 genomes]
rs16855289	0.82[CHD][hapmap]
rs16855295	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs17371159	0.83[TSI][hapmap]
rs17371308	0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs1801795	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4266842	0.87[EUR][1000 genomes]
rs4278337	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4460595	1.00[CEU][hapmap];0.88[YRI][hapmap];0.91[EUR][1000 genomes]
rs4652468	0.81[ASN][1000 genomes]
rs4652469	0.91[CHD][hapmap];0.81[ASN][1000 genomes]
rs59132689	0.85[EUR][1000 genomes]
rs60972670	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61242295	0.88[EUR][1000 genomes]
rs73032390	0.85[EUR][1000 genomes]
rs73032397	0.87[EUR][1000 genomes]
rs73034408	0.87[EUR][1000 genomes]
rs73034486	0.91[EUR][1000 genomes]
rs73036458	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv872573	chr1:179929388-180093066	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv520278	chr1:179945390-180093066	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	nsv1012558	chr1:180027960-180217613	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv535218	chr1:180027960-180217613	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv497930	chr1:180031321-180220723	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv533073	chr1:180031328-180217612	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv916937	chr1:180031328-180220685	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12130489	CPNE7	trans	cerebellum	SCAN
rs12130489	CEP350	Cis_1M	lymphoblastoid	RTeQTL
rs12130489	ASTN1	cis	parietal	SCAN
rs12130489	RALGPS2	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180080600-180090400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:180080600-180091000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr1:180081200-180089800	Weak transcription	Fetal Brain Female	brain
4	chr1:180082000-180092400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:180084000-180096000	Weak transcription	Primary T cells from cord blood	blood
6	chr1:180084800-180094000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:180086600-180100800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:180086600-180102400	Weak transcription	Pancreas	Pancrea
9	chr1:180087000-180097800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:180087200-180092600	Weak transcription	K562	blood
11	chr1:180087200-180095600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:180087200-180095600	Weak transcription	Stomach Mucosa	stomach
13	chr1:180087200-180097000	Weak transcription	Lung	lung
14	chr1:180087200-180097400	Weak transcription	Esophagus	oesophagus
15	chr1:180087600-180092800	Weak transcription	Hela-S3	cervix
16	chr1:180087800-180092200	Weak transcription	NHDF-Ad	bronchial
17	chr1:180087800-180092400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:180087800-180092600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:180088000-180089800	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr1:180088000-180090000	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr1:180088000-180092200	Weak transcription	NHEK	skin
22	chr1:180088200-180089800	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr1:180088800-180089800	Enhancers	Ovary	ovary
24	chr1:180089200-180097400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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