Variant report

Variant	rs685012
Chromosome Location	chr12:50446403-50446404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50442392..50444531-chr12:50445010..50447664,2	K562	blood:
2	chr12:50440879..50447724-chr12:50448390..50454714,11	K562	blood:
3	chr12:50445040..50447038-chr12:50470229..50471817,2	K562	blood:
4	chr12:50445380..50449245-chr12:50449968..50451833,3	MCF-7	breast:
5	chr12:50444648..50446758-chr12:50452831..50455607,2	K562	blood:
6	chr12:50441963..50444884-chr12:50445387..50446910,2	MCF-7	breast:
7	chr12:50431093..50436094-chr12:50443171..50446761,5	K562	blood:

Variant related genes	Relation type
ENSG00000110881	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10875995	0.85[EUR][1000 genomes]
rs10875996	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11169263	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2307084	0.83[CHB][hapmap]
rs376184	0.90[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs404751	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs439171	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs450423	0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs484951	0.90[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap]
rs4898546	0.90[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs56990521	0.85[EUR][1000 genomes]
rs590460	0.83[ASW][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs613066	0.90[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap]
rs706789	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs706794	0.90[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73299515	0.93[EUR][1000 genomes]
rs73299518	0.91[EUR][1000 genomes]
rs7956491	0.93[EUR][1000 genomes]
rs835591	0.80[ASN][1000 genomes]
rs835593	0.81[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap]
rs836175	0.80[AMR][1000 genomes]
rs836178	0.90[CHB][hapmap];0.83[JPT][hapmap];0.90[TSI][hapmap]
rs836184	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs844359	0.81[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap]
rs860699	0.80[ASN][1000 genomes]

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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS 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	28 gene(s)	inside rSNPs	diseases
6	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs685012	LASS5	cis	cerebellum	SCAN
rs685012	AQP6	cis	parietal	SCAN
rs685012	CERS5	cis	Nerve Tibial	GTEx
rs685012	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs685012	SNORA2A	cis	parietal	SCAN
rs685012	ATF1	cis	parietal	SCAN
rs685012	LASS5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50443000-50447200	Enhancers	Fetal Brain Male	brain
2	chr12:50444400-50449600	Weak transcription	Brain Angular Gyrus	brain
3	chr12:50444400-50449600	Weak transcription	Gastric	stomach
4	chr12:50444400-50449600	Weak transcription	Spleen	Spleen
5	chr12:50444400-50450800	Weak transcription	Lung	lung
6	chr12:50444600-50449400	Weak transcription	Brain Anterior Caudate	brain
7	chr12:50444600-50449600	Weak transcription	Brain Hippocampus Middle	brain
8	chr12:50444600-50449600	Weak transcription	Brain Substantia Nigra	brain
9	chr12:50444600-50449600	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:50444600-50449600	Weak transcription	Pancreas	Pancrea
11	chr12:50444800-50447800	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr12:50444800-50450800	Weak transcription	Right Atrium	heart
13	chr12:50445200-50446600	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr12:50445200-50447600	Enhancers	Brain Germinal Matrix	brain
15	chr12:50445200-50449600	Weak transcription	Ovary	ovary
16	chr12:50445400-50447800	Enhancers	Fetal Brain Female	brain
17	chr12:50445400-50448000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:50445400-50449600	Weak transcription	Right Ventricle	heart
19	chr12:50445400-50450000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:50445600-50447000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:50445600-50447400	Weak transcription	Fetal Heart	heart
22	chr12:50445800-50449600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:50446200-50446800	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr12:50446400-50447400	Enhancers	Cortex derived primary cultured neurospheres	brain

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