Variant report

Variant	rs835592
Chromosome Location	chr12:50460831-50460832
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50434366..50436539-chr12:50459829..50461923,2	MCF-7	breast:
2	chr12:50460036..50462356-chr12:50466641..50469491,3	MCF-7	breast:
3	chr12:50459247..50461166-chr12:50463048..50465516,2	K562	blood:
4	chr12:50417744..50420725-chr12:50458618..50461383,3	K562	blood:
5	chr12:50452088..50458692-chr12:50460164..50465883,8	K562	blood:

Variant related genes	Relation type
ENSG00000110881	Chromatin interaction
ENSG00000161800	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1044370	0.88[CEU][hapmap]
rs1979702	0.96[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs2272391	0.92[CEU][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs578470	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs646782	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs706790	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs706791	0.92[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs706792	0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs706793	0.80[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7279	0.80[TSI][hapmap]
rs7532	0.80[TSI][hapmap]
rs836172	0.96[CEU][hapmap];0.95[TSI][hapmap]
rs836177	0.96[CEU][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap]
rs836180	0.80[TSI][hapmap]
rs836188	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836189	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs844347	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs860698	0.96[CEU][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap]

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	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
8	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
9	nsv437753	chr12:50454357-50462138	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs835592	LASS5	cis	cerebellum	SCAN
rs835592	LASS5	cis	parietal	SCAN
rs835592	TMEM106C	cis	cerebellum	SCAN
rs835592	CERS5	cis	Nerve Tibial	GTEx
rs835592	SLC38A1	cis	parietal	SCAN
rs835592	LASS5	cis	multi-tissue	Pritchard
rs835592	MCRS1	cis	parietal	SCAN
rs835592	SNORA2A	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50451400-50464000	Weak transcription	Fetal Lung	lung
2	chr12:50451800-50464200	Weak transcription	Gastric	stomach
3	chr12:50452000-50464200	Weak transcription	A549	lung
4	chr12:50452200-50464000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:50452600-50464000	Weak transcription	Esophagus	oesophagus
6	chr12:50454600-50464200	Weak transcription	Fetal Intestine Small	intestine
7	chr12:50454800-50464000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:50455600-50464200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:50455800-50464000	Weak transcription	Adipose Nuclei	Adipose
10	chr12:50456600-50463800	Weak transcription	Dnd41	blood
11	chr12:50457400-50464000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:50458000-50461600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr12:50458200-50478200	Weak transcription	Thymus	Thymus
14	chr12:50458800-50463800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:50459200-50461200	Enhancers	Colon Smooth Muscle	Colon
16	chr12:50459400-50461000	Enhancers	NHDF-Ad	bronchial
17	chr12:50459400-50461600	Weak transcription	Fetal Brain Female	brain
18	chr12:50459600-50461000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:50459600-50463800	Weak transcription	Brain Hippocampus Middle	brain
20	chr12:50459600-50465000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:50459800-50461000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:50459800-50461000	Enhancers	Fetal Heart	heart
23	chr12:50459800-50461000	Enhancers	HSMMtube	muscle
24	chr12:50459800-50463800	Weak transcription	Fetal Brain Male	brain
25	chr12:50460000-50461000	Enhancers	HSMM	muscle
26	chr12:50460000-50461200	Enhancers	NHLF	lung
27	chr12:50460000-50461400	Enhancers	Rectal Smooth Muscle	rectum
28	chr12:50460000-50464000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr12:50460200-50461000	Enhancers	Muscle Satellite Cultured Cells	--
30	chr12:50460200-50461000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:50460200-50464000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr12:50460200-50464000	Weak transcription	Brain Angular Gyrus	brain
33	chr12:50460200-50464200	Weak transcription	Primary T cells from cord blood	blood
34	chr12:50460400-50461000	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr12:50460400-50462400	Weak transcription	Fetal Stomach	stomach
36	chr12:50460400-50464000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:50460400-50464000	Weak transcription	Fetal Muscle Trunk	muscle
38	chr12:50460400-50464000	Weak transcription	Right Atrium	heart
39	chr12:50460600-50463800	Weak transcription	Brain Anterior Caudate	brain
40	chr12:50460600-50463800	Weak transcription	Hela-S3	cervix
41	chr12:50460600-50464000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:50460600-50464000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:50460600-50464000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:50460600-50464000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:50460600-50464000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr12:50460600-50464000	Weak transcription	Brain Substantia Nigra	brain
47	chr12:50460600-50464000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr12:50460600-50464000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr12:50460600-50464200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr12:50460600-50464200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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