Variant report

Variant	rs1376341
Chromosome Location	chr12:62802643-62802644
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:62802223..62804398-chr12:62996125..62998801,2	K562	blood:
2	chr12:62802154..62805925-chr12:62805959..62810469,4	K562	blood:
3	chr12:62800166..62802965-chr12:62803094..62805711,2	K562	blood:
4	chr12:62802231..62804396-chr12:62807395..62808972,2	K562	blood:

Variant related genes	Relation type
ENSG00000199179	Chromatin interaction
ENSG00000221949	Chromatin interaction
ENSG00000257354	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1032417	0.81[CEU][hapmap]
rs10747960	0.85[CHB][hapmap]
rs10747962	0.99[ASN][1000 genomes]
rs10784290	0.81[CEU][hapmap]
rs10784291	0.81[CEU][hapmap]
rs10877819	0.82[YRI][hapmap]
rs11174449	0.87[LWK][hapmap];0.96[MKK][hapmap];0.82[YRI][hapmap]
rs11174477	0.89[ASN][1000 genomes]
rs12424732	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs1512024	0.81[CEU][hapmap]
rs1566079	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2044846	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2122659	0.80[CEU][hapmap]
rs7312513	0.81[CEU][hapmap]
rs7315790	0.81[CEU][hapmap]
rs7953445	0.81[CEU][hapmap]
rs7954439	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7956101	0.81[CEU][hapmap]
rs7974980	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053403	chr12:62657011-62809413	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv899153	chr12:62716330-62817736	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv1803510	chr12:62729782-62802643	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv469417	chr12:62751242-62802643	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv559155	chr12:62751242-62802643	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv899154	chr12:62764909-62811328	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
8	nsv899155	chr12:62764909-62817736	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv899156	chr12:62783967-62831343	Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
10	nsv899157	chr12:62783967-62843620	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv899158	chr12:62783967-62937259	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
12	nsv899159	chr12:62783967-62945245	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
13	nsv821671	chr12:62794304-63007964	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1376341	LRP1	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62763000-62805400	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr12:62767400-62807600	Weak transcription	HSMMtube	muscle
3	chr12:62769200-62805000	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr12:62769400-62809600	Weak transcription	Stomach Mucosa	stomach
5	chr12:62774800-62803200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr12:62775600-62807800	Weak transcription	Aorta	Aorta
7	chr12:62783400-62803400	Weak transcription	NHEK	skin
8	chr12:62787800-62803600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:62791600-62807000	Weak transcription	Esophagus	oesophagus
10	chr12:62793200-62803400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr12:62794200-62805800	Weak transcription	NHLF	lung
12	chr12:62796400-62805200	Weak transcription	NH-A	brain
13	chr12:62796600-62807400	Weak transcription	A549	lung
14	chr12:62797200-62803400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:62797400-62809200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:62797800-62803400	Weak transcription	Osteobl	bone
17	chr12:62798200-62806400	Weak transcription	Left Ventricle	heart
18	chr12:62798200-62807400	Weak transcription	Thymus	Thymus
19	chr12:62798400-62809400	Weak transcription	HSMM	muscle
20	chr12:62798600-62803000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr12:62798800-62803200	Weak transcription	Fetal Lung	lung
22	chr12:62798800-62803400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:62799200-62803200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:62799200-62807200	Weak transcription	HUVEC	blood vessel
25	chr12:62799200-62809200	Weak transcription	Fetal Brain Female	brain
26	chr12:62799400-62802800	Weak transcription	Adipose Nuclei	Adipose
27	chr12:62799400-62803600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr12:62799400-62804800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr12:62799400-62806000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:62799400-62806200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr12:62799400-62808600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:62799400-62808600	Weak transcription	HMEC	breast
33	chr12:62799400-62809000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:62799600-62802800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr12:62799600-62803200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:62799600-62803200	Weak transcription	Fetal Intestine Large	intestine
37	chr12:62799600-62803400	Weak transcription	Hela-S3	cervix
38	chr12:62799600-62804400	Weak transcription	NHDF-Ad	bronchial
39	chr12:62799800-62806400	Weak transcription	Placenta	Placenta
40	chr12:62800800-62803600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr12:62800800-62806400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:62801000-62806000	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr12:62801200-62802800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:62801200-62802800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr12:62801200-62806600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:62801200-62808000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:62801600-62803200	Weak transcription	K562	blood
48	chr12:62801600-62804800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:62801800-62808000	Weak transcription	GM12878-XiMat	blood
50	chr12:62802000-62802800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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