Variant report

Variant	rs12058931
Chromosome Location	chr1:154825093-154825094
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154823084..154826737-chr1:154829485..154832130,3	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11264275	0.83[CHD][hapmap]
rs11586348	1.00[JPT][hapmap]
rs12084791	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12089942	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128882	1.00[JPT][hapmap]
rs1218566	1.00[JPT][hapmap]
rs12729486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13376333	1.00[JPT][hapmap]
rs34245846	0.85[ASN][1000 genomes]
rs4492614	1.00[CHB][hapmap]
rs56382016	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6426985	1.00[JPT][hapmap]
rs6426987	1.00[JPT][hapmap]
rs6426988	1.00[JPT][hapmap]
rs6666258	1.00[JPT][hapmap]
rs6666891	1.00[JPT][hapmap]
rs6704449	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv432931	chr1:154794318-154855055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	esv29982	chr1:154818353-154882544	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv432942	chr1:154818353-154903047	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv432964	chr1:154820067-154849590	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv432953	chr1:154820067-154855055	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12058931	HAPLN2	cis	parietal	SCAN
rs12058931	SNAPIN	cis	cerebellum	SCAN
rs12058931	VPS72	cis	cerebellum	SCAN
rs12058931	OAZ3	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154819200-154828400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:154820000-154826000	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr1:154820800-154832600	Weak transcription	Right Atrium	heart
4	chr1:154821000-154832000	Weak transcription	HSMM	muscle
5	chr1:154821000-154837200	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:154821200-154828400	Weak transcription	Psoas Muscle	Psoas
7	chr1:154821200-154828400	Weak transcription	Spleen	Spleen
8	chr1:154821200-154828800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:154821400-154825200	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr1:154822000-154828000	Weak transcription	Brain Substantia Nigra	brain
11	chr1:154822200-154828000	Weak transcription	Fetal Stomach	stomach
12	chr1:154822600-154838000	Weak transcription	Brain Angular Gyrus	brain
13	chr1:154822800-154826800	Weak transcription	Fetal Brain Female	brain
14	chr1:154822800-154828200	Weak transcription	HSMMtube	muscle
15	chr1:154822800-154832200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:154823000-154828000	Weak transcription	Brain Anterior Caudate	brain
17	chr1:154823000-154828600	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:154823000-154830600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:154823200-154827800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:154823200-154828000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:154823200-154828400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:154823400-154827800	Weak transcription	Brain Germinal Matrix	brain
23	chr1:154823400-154832400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:154824200-154825200	Weak transcription	Fetal Muscle Leg	muscle
25	chr1:154824200-154828200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr1:154824400-154834200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:154824600-154827000	Weak transcription	Fetal Brain Male	brain
28	chr1:154825000-154825400	Weak transcription	GM12878-XiMat	blood

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