Variant report

Variant	rs6430301
Chromosome Location	chr2:148953669-148953670
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10171170	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10173542	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10180469	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10191634	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10497028	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10497031	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10803524	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10928384	0.81[GIH][hapmap]
rs1227479	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1227482	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1227484	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1234398	0.82[JPT][hapmap]
rs1234399	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1234400	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1234403	0.83[EUR][1000 genomes]
rs1234404	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1234431	0.89[ASN][1000 genomes]
rs12619583	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994189	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs4972323	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4972324	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4972336	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59094777	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59984641	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60850392	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183893	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62183896	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62183921	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62183924	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183925	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183933	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6430293	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6430294	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6711560	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714702	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6715654	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6750841	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7571453	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7574172	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7578002	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602932	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916286	chr2:148438001-148977722	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv916766	chr2:148743880-148955720	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1001339	chr2:148755022-149020866	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv535977	chr2:148755022-149020866	Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv869146	chr2:148787051-149060763	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv875276	chr2:148844369-148996824	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1004431	chr2:148859099-149054114	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv997674	chr2:148862630-148995570	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1007998	chr2:148866051-148995570	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1009608	chr2:148897348-149133718	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv915953	chr2:148934787-148977722	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6430301	LYPD6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148913000-148977600	Weak transcription	Aorta	Aorta
2	chr2:148925200-148959000	Weak transcription	Brain Hippocampus Middle	brain
3	chr2:148928600-148993600	Weak transcription	HSMM	muscle
4	chr2:148929800-148960800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr2:148931000-148960600	Weak transcription	Spleen	Spleen
6	chr2:148931200-148958600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:148931200-148993200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:148938400-148958600	Weak transcription	Fetal Intestine Small	intestine
9	chr2:148938400-148969200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:148939000-148958600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:148941000-148958600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:148941200-148959400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:148942800-148958600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:148942800-148958800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:148943800-148961200	Weak transcription	Fetal Lung	lung
16	chr2:148944000-148987400	Weak transcription	Ovary	ovary
17	chr2:148944200-148978400	Weak transcription	Left Ventricle	heart
18	chr2:148944400-148962200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr2:148944600-148978400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:148944800-148957400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:148945200-148958600	Weak transcription	Primary B cells from cord blood	blood
22	chr2:148946200-148958800	Weak transcription	Primary T cells from cord blood	blood
23	chr2:148952600-148958600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:148953400-148953800	Enhancers	Primary neutrophils fromperipheralblood	blood

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