Variant report

Variant	rs6740838
Chromosome Location	chr2:100813499-100813500
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10167029	0.97[ASN][1000 genomes]
rs10167279	0.99[ASN][1000 genomes]
rs10194635	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10865035	0.85[ASN][1000 genomes]
rs1160542	0.89[ASN][1000 genomes]
rs1160544	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11676922	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11677053	0.91[ASN][1000 genomes]
rs11687241	0.86[CHB][hapmap]
rs11689199	0.84[CHB][hapmap]
rs11689201	0.85[CHB][hapmap]
rs12712073	0.87[ASN][1000 genomes]
rs2309837	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4851267	0.82[CHB][hapmap]
rs4851269	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6712515	0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6722241	0.86[ASN][1000 genomes]
rs6740612	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6754937	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7580200	0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs893245	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9653442	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003343	chr2:100241560-100848900	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535843	chr2:100241560-100848900	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6740838	ASTL	cis	cerebellum	SCAN
rs6740838	AFF3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100800000-100814000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:100801800-100813600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:100806200-100814200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:100809600-100815600	Enhancers	Fetal Lung	lung
5	chr2:100809800-100814200	Enhancers	Adipose Nuclei	Adipose
6	chr2:100810000-100813600	Weak transcription	NHDF-Ad	bronchial
7	chr2:100810200-100813600	Weak transcription	HSMMtube	muscle
8	chr2:100810200-100814000	Weak transcription	NH-A	brain
9	chr2:100810200-100814400	Weak transcription	K562	blood
10	chr2:100810600-100814000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr2:100810600-100814000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:100810600-100814200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:100810600-100814200	Weak transcription	Psoas Muscle	Psoas
14	chr2:100810800-100813600	Weak transcription	HUVEC	blood vessel
15	chr2:100810800-100814200	Weak transcription	Stomach Mucosa	stomach
16	chr2:100811600-100814200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:100811800-100816600	Enhancers	Lung	lung
18	chr2:100812200-100815600	Enhancers	Right Ventricle	heart
19	chr2:100812200-100816000	Enhancers	Fetal Muscle Trunk	muscle
20	chr2:100812400-100813600	Weak transcription	Fetal Intestine Small	intestine
21	chr2:100812400-100814400	Enhancers	Rectal Smooth Muscle	rectum
22	chr2:100812400-100814600	Enhancers	Colon Smooth Muscle	Colon
23	chr2:100812400-100815600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr2:100812400-100815600	Enhancers	Left Ventricle	heart
25	chr2:100812400-100815800	Enhancers	Placenta	Placenta
26	chr2:100812600-100813600	Weak transcription	Ovary	ovary
27	chr2:100812600-100815800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:100812800-100813600	Weak transcription	Right Atrium	heart
29	chr2:100812800-100814000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:100812800-100814200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:100812800-100814200	Weak transcription	Aorta	Aorta
32	chr2:100812800-100814200	Enhancers	Stomach Smooth Muscle	stomach
33	chr2:100812800-100815600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:100812800-100815800	Enhancers	Fetal Muscle Leg	muscle
35	chr2:100813200-100814200	Weak transcription	Pancreas	Pancrea
36	chr2:100813400-100813600	Enhancers	Osteobl	bone
37	chr2:100813400-100814200	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr2:100813400-100815000	Enhancers	Fetal Heart	heart
39	chr2:100813400-100815200	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr2:100813400-100815400	Enhancers	Fetal Intestine Large	intestine
41	chr2:100813400-100815400	Enhancers	Fetal Stomach	stomach
42	chr2:100813400-100816200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:100813400-100817000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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