Variant report

Variant	rs12143905
Chromosome Location	chr1:79351020-79351021
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10157320	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs10158148	0.87[CEU][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs10493618	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs10782673	0.89[CEU][hapmap]
rs11162577	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11162583	0.85[CEU][hapmap];0.90[YRI][hapmap];0.87[EUR][1000 genomes]
rs11162584	0.87[EUR][1000 genomes]
rs11587450	0.86[CEU][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12030712	0.87[EUR][1000 genomes]
rs12031706	0.88[EUR][1000 genomes]
rs12032838	0.87[CEU][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12123867	0.82[EUR][1000 genomes]
rs12142366	0.90[ASW][hapmap];0.87[CEU][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];0.80[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12402432	0.87[CEU][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1332831	0.87[CEU][hapmap]
rs1352555	0.87[CEU][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs1387421	0.86[CEU][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1387422	0.90[CEU][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1489386	0.87[CEU][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1489391	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs1489402	0.87[CEU][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1489403	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs17403208	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17403465	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17414239	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs2130193	0.86[EUR][1000 genomes]
rs2130199	0.86[CEU][hapmap]
rs2275902	0.87[CEU][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2352614	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2635119	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3811440	0.88[EUR][1000 genomes]
rs4387133	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6424621	0.81[ASW][hapmap];0.87[CEU][hapmap];0.97[GIH][hapmap];0.86[LWK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes]
rs6660288	0.87[CEU][hapmap]
rs6668563	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs7512011	0.87[CEU][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7532212	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7533063	0.86[CEU][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7552978	0.90[ASW][hapmap];0.87[CEU][hapmap];0.97[GIH][hapmap];0.98[LWK][hapmap];0.80[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv491784	chr1:79146141-79853482	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv526221	chr1:79197624-79487080	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv817535	chr1:79203834-79473089	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv999624	chr1:79230028-79448222	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv535013	chr1:79230028-79448222	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv546619	chr1:79233493-79614989	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv2830430	chr1:79310760-79555593	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1010441	chr1:79320299-79555315	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12143905	ST20	trans	parietal	SCAN
rs12143905	NEXN	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79348600-79405600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:79350200-79351200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:79350200-79351200	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr1:79350200-79351400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:79350200-79351400	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr1:79350400-79351200	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr1:79350400-79351200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:79350400-79351200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:79350400-79351200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:79350400-79351200	Flanking Active TSS	Hela-S3	cervix
11	chr1:79350400-79351200	Enhancers	NH-A	brain
12	chr1:79350400-79351400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr1:79350400-79351400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:79350400-79351600	Enhancers	Muscle Satellite Cultured Cells	--
15	chr1:79350600-79351200	Enhancers	H1 Cell Line	embryonic stem cell
16	chr1:79350600-79351200	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr1:79350600-79351200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:79350600-79351200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:79350600-79351200	Enhancers	Stomach Smooth Muscle	stomach
20	chr1:79350600-79351600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:79350800-79351200	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr1:79350800-79351200	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr1:79350800-79351200	Enhancers	NHDF-Ad	bronchial
24	chr1:79350800-79358600	Strong transcription	HUVEC	blood vessel
25	chr1:79351000-79360800	Weak transcription	Left Ventricle	heart
26	chr1:79351000-79365600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:79351000-79367600	Weak transcription	Adipose Nuclei	Adipose

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