Variant report

Variant	rs12141928
Chromosome Location	chr1:46677918-46677919
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46676099..46679666-chr1:46685749..46689676,3	K562	blood:
2	chr1:46108295..46110587-chr1:46677470..46679622,2	K562	blood:
3	chr1:46622851..46625165-chr1:46677370..46678952,2	K562	blood:
4	chr1:46675947..46678280-chr1:46679542..46682486,2	K562	blood:
5	chr1:46677363..46679739-chr1:46682959..46684489,2	K562	blood:

Variant related genes	Relation type
ENSG00000085998	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10789488	0.94[MEX][hapmap]
rs10890386	0.94[MEX][hapmap]
rs10890388	0.81[CEU][hapmap];0.94[MEX][hapmap]
rs12028248	0.94[MEX][hapmap];0.89[TSI][hapmap]
rs12116820	0.89[ASN][1000 genomes]
rs12125573	0.93[MEX][hapmap]
rs12126187	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12132921	0.90[ASN][1000 genomes]
rs12141269	0.89[CHB][hapmap];0.94[MEX][hapmap];0.81[AMR][1000 genomes]
rs12406217	0.89[CHB][hapmap];0.81[AMR][1000 genomes]
rs1547180	0.94[MEX][hapmap];0.82[MKK][hapmap]
rs2292484	0.81[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs2292485	0.90[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs2292487	0.90[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs35865534	0.97[ASN][1000 genomes]
rs4612574	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4660918	0.81[CEU][hapmap];0.94[MEX][hapmap]
rs4660919	0.94[MEX][hapmap]
rs4660921	0.94[MEX][hapmap]
rs6429594	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66462608	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6689182	0.82[MEX][hapmap]
rs6692775	0.89[TSI][hapmap];0.82[AMR][1000 genomes]
rs6696085	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7519275	0.89[ASN][1000 genomes]
rs7521617	0.97[ASN][1000 genomes]
rs7521880	0.90[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs7527668	0.90[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs7527935	0.89[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs7538871	0.90[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs7552312	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7552589	0.89[ASN][1000 genomes]
rs953070	0.94[MEX][hapmap];0.89[TSI][hapmap]
rs953823	0.90[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv470711	chr1:46660295-46810530	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12141928	CLDN19	cis	cerebellum	SCAN
rs12141928	MMACHC	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46670400-46685400	Weak transcription	Aorta	Aorta
2	chr1:46670400-46685400	Weak transcription	Brain Germinal Matrix	brain
3	chr1:46670400-46689000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:46670400-46689400	Weak transcription	HSMM	muscle
5	chr1:46670600-46680400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:46670600-46684000	Weak transcription	Fetal Stomach	stomach
7	chr1:46670600-46684200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:46670600-46687200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:46670600-46689400	Weak transcription	Osteobl	bone
10	chr1:46671000-46689400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:46671600-46689000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:46671800-46683600	Weak transcription	NHEK	skin
13	chr1:46671800-46685200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:46671800-46685400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:46671800-46689000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr1:46672400-46684200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:46672400-46689400	Weak transcription	Left Ventricle	heart
18	chr1:46672600-46684000	Weak transcription	Brain Substantia Nigra	brain
19	chr1:46672600-46684200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:46672600-46685000	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:46672600-46685000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:46672600-46685400	Weak transcription	Brain Anterior Caudate	brain
23	chr1:46672600-46689400	Weak transcription	Ovary	ovary
24	chr1:46672800-46684200	Weak transcription	Fetal Brain Female	brain
25	chr1:46672800-46685600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:46672800-46686400	Weak transcription	Colon Smooth Muscle	Colon
27	chr1:46672800-46689400	Weak transcription	Right Ventricle	heart
28	chr1:46673000-46683200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:46673000-46685200	Weak transcription	Brain Angular Gyrus	brain
30	chr1:46673000-46685200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:46673000-46712200	Weak transcription	Right Atrium	heart
32	chr1:46674000-46683800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:46674600-46683800	Weak transcription	HMEC	breast
34	chr1:46675600-46682000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:46676200-46685200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr1:46676400-46683600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:46676600-46678000	Enhancers	K562	blood
38	chr1:46676600-46685400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:46677000-46686800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:46677800-46679000	Weak transcription	Fetal Heart	heart

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