Variant report

Variant	rs6711560
Chromosome Location	chr2:148927024-148927025
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10171170	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10173542	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10180469	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10191634	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10497028	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10497031	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10803524	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10928384	0.81[GIH][hapmap];0.81[JPT][hapmap]
rs1227479	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1227482	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1227484	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1234398	0.90[JPT][hapmap]
rs1234399	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1234400	0.86[ASN][1000 genomes]
rs1234403	0.81[EUR][1000 genomes]
rs1234404	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1234414	0.81[JPT][hapmap]
rs1234431	0.89[ASN][1000 genomes]
rs12619583	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994189	0.88[CHD][hapmap];0.90[JPT][hapmap]
rs4972323	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4972324	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4972336	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59094777	0.89[ASN][1000 genomes]
rs59984641	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60850392	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183893	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62183896	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62183921	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62183924	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183925	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183933	0.92[ASN][1000 genomes]
rs6430293	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6430294	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6430301	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714702	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6715654	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6750841	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7571453	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7574172	0.81[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7578002	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583240	0.87[AFR][1000 genomes]
rs7602932	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv529388	chr2:148471340-148934846	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1002358	chr2:148703807-148942372	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1007683	chr2:148717347-148942372	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535971	chr2:148717347-148942372	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1000852	chr2:148730825-148934986	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS 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
7	nsv535972	chr2:148730825-148934986	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv999952	chr2:148884787-148938697	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
17	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6711560	LYPD6	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148906000-148937000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:148911400-148942400	Weak transcription	Ovary	ovary
3	chr2:148913000-148977600	Weak transcription	Aorta	Aorta
4	chr2:148913400-148930400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:148914800-148936000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:148915000-148937000	Weak transcription	Adipose Nuclei	Adipose
7	chr2:148915200-148929600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:148915400-148929600	Weak transcription	Fetal Intestine Small	intestine
9	chr2:148916800-148938600	Weak transcription	Primary B cells from cord blood	blood
10	chr2:148917200-148928400	Weak transcription	Primary T cells from cord blood	blood
11	chr2:148917200-148929400	Weak transcription	Fetal Stomach	stomach
12	chr2:148917800-148937200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:148918800-148938000	Weak transcription	Fetal Lung	lung
14	chr2:148919800-148945800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:148920000-148937000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr2:148924000-148930000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:148924200-148941800	Weak transcription	Brain Angular Gyrus	brain
18	chr2:148924400-148938000	Weak transcription	Fetal Kidney	kidney
19	chr2:148924400-148946400	Weak transcription	HSMMtube	muscle
20	chr2:148924600-148936400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:148924600-148946800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:148925000-148929400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:148925200-148959000	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:148925400-148936200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:148926000-148938000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:148927000-148940400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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