Variant report

Variant	rs7742707
Chromosome Location	chr6:144223021-144223022
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12527718	0.82[CHB][hapmap];0.96[ASN][1000 genomes]
rs12527740	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs35274932	0.96[ASN][1000 genomes]
rs4140441	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4895623	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4896684	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4896685	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4896686	1.00[CHB][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6570586	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs761540	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs761541	1.00[CHB][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs764667	0.82[CHB][hapmap];0.96[ASN][1000 genomes]
rs7755147	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9484827	1.00[JPT][hapmap]
rs9496799	0.82[CHB][hapmap];0.86[AFR][1000 genomes]
rs9496805	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3408554	chr6:144106707-144369589	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3522138	chr6:144174685-144367463	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv3522139	chr6:144174685-144367463	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv830830	chr6:144177942-144380870	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7742707	LTV1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144218400-144224000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:144219200-144234200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:144221200-144239200	Weak transcription	Primary B cells from cord blood	blood
4	chr6:144222000-144225000	Enhancers	Fetal Lung	lung
5	chr6:144222200-144225000	Enhancers	Fetal Muscle Leg	muscle
6	chr6:144222400-144225000	Enhancers	Ovary	ovary
7	chr6:144222600-144223800	Enhancers	Fetal Intestine Small	intestine
8	chr6:144222600-144224600	Enhancers	Fetal Stomach	stomach
9	chr6:144222800-144223400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr6:144222800-144223400	Enhancers	Small Intestine	intestine
11	chr6:144222800-144223800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:144222800-144223800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:144222800-144223800	Enhancers	Aorta	Aorta
14	chr6:144222800-144223800	Enhancers	Brain Anterior Caudate	brain
15	chr6:144222800-144223800	Enhancers	Rectal Smooth Muscle	rectum
16	chr6:144222800-144224000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr6:144222800-144224200	Enhancers	Brain Hippocampus Middle	brain
18	chr6:144222800-144224200	Enhancers	Colon Smooth Muscle	Colon
19	chr6:144222800-144224200	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr6:144222800-144224200	Flanking Active TSS	GM12878-XiMat	blood
21	chr6:144222800-144224400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:144222800-144224400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:144222800-144224400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:144222800-144224400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:144222800-144224400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr6:144222800-144224400	Enhancers	Fetal Kidney	kidney
27	chr6:144222800-144224400	Enhancers	Placenta	Placenta
28	chr6:144222800-144225000	Enhancers	Adipose Nuclei	Adipose
29	chr6:144223000-144223200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:144223000-144223200	Enhancers	Primary B cells from peripheral blood	blood
31	chr6:144223000-144223200	Enhancers	Brain Cingulate Gyrus	brain
32	chr6:144223000-144223200	Active TSS	Stomach Smooth Muscle	stomach
33	chr6:144223000-144223400	Enhancers	Brain Angular Gyrus	brain
34	chr6:144223000-144223400	Flanking Active TSS	Brain Substantia Nigra	brain
35	chr6:144223000-144223600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:144223000-144223600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr6:144223000-144223600	Enhancers	NHDF-Ad	bronchial
38	chr6:144223000-144223800	Flanking Active TSS	HSMMtube	muscle
39	chr6:144223000-144224200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:144223000-144224200	Enhancers	Right Atrium	heart
41	chr6:144223000-144224400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:144223000-144224400	Active TSS	Fetal Brain Male	brain
43	chr6:144223000-144224400	Enhancers	NHLF	lung

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