Variant report

Variant	rs1058840
Chromosome Location	chr2:33540248-33540249
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10191688	0.87[YRI][hapmap];0.81[AFR][1000 genomes]
rs2276591	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs7580131	0.94[ASW][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998167	chr2:33074313-33541100	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535623	chr2:33074313-33541100	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer 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	24 gene(s)	inside rSNPs	diseases
3	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
5	nsv873791	chr2:33489975-33586776	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	nsv1012967	chr2:33533340-33638312	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv535627	chr2:33533340-33638312	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1058840	SLC30A6	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33492400-33547400	Weak transcription	Fetal Intestine Small	intestine
2	chr2:33517200-33545000	Weak transcription	Fetal Kidney	kidney
3	chr2:33517200-33545800	Weak transcription	Fetal Lung	lung
4	chr2:33517200-33546400	Weak transcription	Brain Angular Gyrus	brain
5	chr2:33517800-33543400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:33523400-33545200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:33523600-33546200	Weak transcription	K562	blood
8	chr2:33523800-33550600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:33524200-33546600	Weak transcription	Small Intestine	intestine
10	chr2:33529000-33541400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:33529600-33546400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:33529800-33546600	Weak transcription	Psoas Muscle	Psoas
13	chr2:33529800-33561000	Weak transcription	HUVEC	blood vessel
14	chr2:33529800-33609400	Weak transcription	Right Ventricle	heart
15	chr2:33530000-33543000	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:33531800-33540400	Weak transcription	Liver	Liver
17	chr2:33533400-33542800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:33535600-33544600	Weak transcription	NHLF	lung
19	chr2:33537400-33545800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:33537800-33540400	Enhancers	HMEC	breast
21	chr2:33538400-33540400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:33538400-33541000	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:33538400-33541800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:33538400-33543200	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr2:33538400-33545600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:33538400-33545800	Strong transcription	Osteobl	bone
27	chr2:33538600-33540600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:33538600-33541600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:33538600-33541800	Weak transcription	NHDF-Ad	bronchial
30	chr2:33538800-33541600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:33538800-33542600	Weak transcription	Ovary	ovary
32	chr2:33539000-33541000	Strong transcription	Fetal Stomach	stomach
33	chr2:33539000-33542600	Weak transcription	Lung	lung
34	chr2:33539000-33544800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:33539400-33542000	Weak transcription	Esophagus	oesophagus
36	chr2:33539400-33542600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:33539600-33540600	Genic enhancers	Fetal Heart	heart
38	chr2:33539600-33541000	Strong transcription	Aorta	Aorta
39	chr2:33539600-33545600	Weak transcription	Fetal Muscle Leg	muscle
40	chr2:33539800-33541000	Strong transcription	Stomach Smooth Muscle	stomach
41	chr2:33539800-33543600	Strong transcription	NH-A	brain
42	chr2:33540000-33540800	Strong transcription	Placenta	Placenta
43	chr2:33540000-33541200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:33540200-33541000	Strong transcription	Left Ventricle	heart

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