Variant report

Variant	rs6544338
Chromosome Location	chr2:40660209-40660210
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10164458	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4411757	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4557029	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4557030	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4952414	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4952619	0.83[AMR][1000 genomes]
rs4952620	0.94[CHD][hapmap];1.00[JPT][hapmap]
rs6719806	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6719986	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6737745	0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7349326	0.83[ASN][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	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2757794	chr2:40547947-40733776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759044	chr2:40547947-40733776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6544338	SULT6B1	cis	parietal	SCAN
rs6544338	ABCG5	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40646600-40670800	Weak transcription	Fetal Brain Female	brain
2	chr2:40647600-40662200	Weak transcription	Brain Germinal Matrix	brain
3	chr2:40648000-40667200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:40648200-40676400	Weak transcription	Fetal Kidney	kidney
5	chr2:40653000-40674800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:40654200-40662200	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:40655000-40665000	Weak transcription	Fetal Brain Male	brain
8	chr2:40657000-40671200	Weak transcription	Fetal Stomach	stomach
9	chr2:40657200-40660600	Enhancers	Rectal Smooth Muscle	rectum
10	chr2:40657200-40662000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:40657800-40663000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:40657800-40666600	Enhancers	Colon Smooth Muscle	Colon
13	chr2:40658000-40660800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:40658000-40663600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:40658000-40664000	Enhancers	NHDF-Ad	bronchial
16	chr2:40658000-40664200	Enhancers	HMEC	breast
17	chr2:40658200-40660400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr2:40658200-40661800	Enhancers	HSMMtube	muscle
19	chr2:40658200-40662200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:40658200-40663400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:40658200-40663600	Enhancers	Osteobl	bone
22	chr2:40658200-40665400	Enhancers	NHLF	lung
23	chr2:40658400-40661400	Enhancers	Stomach Smooth Muscle	stomach
24	chr2:40658400-40663600	Enhancers	Adipose Nuclei	Adipose
25	chr2:40658600-40661800	Enhancers	NHEK	skin
26	chr2:40658600-40663400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:40658600-40663800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:40658800-40661200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:40658800-40662000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:40658800-40662800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:40659000-40660600	Weak transcription	HUVEC	blood vessel
32	chr2:40659000-40660800	Weak transcription	Right Ventricle	heart
33	chr2:40659000-40662200	Weak transcription	Ovary	ovary
34	chr2:40659200-40660800	Weak transcription	Fetal Muscle Leg	muscle
35	chr2:40659200-40661000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:40659200-40661600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:40659200-40661600	Enhancers	Muscle Satellite Cultured Cells	--
38	chr2:40659200-40662000	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr2:40659200-40662000	Weak transcription	Brain Anterior Caudate	brain
40	chr2:40659200-40663400	Enhancers	Hela-S3	cervix
41	chr2:40659600-40661000	Weak transcription	NH-A	brain
42	chr2:40659600-40663200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:40659800-40662000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:40659800-40662000	Weak transcription	Right Atrium	heart
45	chr2:40659800-40664000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:40659800-40665600	Weak transcription	Dnd41	blood
47	chr2:40660000-40660800	Weak transcription	Left Ventricle	heart
48	chr2:40660000-40661000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr2:40660000-40662000	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr2:40660000-40663200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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