Variant report

Variant	rs2500540
Chromosome Location	chr6:149330806-149330807
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10080240	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1343742	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1934224	0.82[GIH][hapmap]
rs2185248	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2340750	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2449385	0.86[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2486387	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2486388	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2486389	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2486393	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2486394	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2486399	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs2486419	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2486420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2500523	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs2500524	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2500527	0.86[EUR][1000 genomes]
rs2500529	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2500531	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2500532	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2500534	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2500537	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2500538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2500541	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2500549	0.85[JPT][hapmap]
rs6911303	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs7759757	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[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	nsv1032690	chr6:149206106-149398712	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv830842	chr6:149272321-149427340	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2500540	PLEKHG1	cis	cerebellum	SCAN
rs2500540	C6orf211	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149305400-149381400	Weak transcription	Gastric	stomach
2	chr6:149310200-149335200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:149311000-149335200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:149320200-149335400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:149320200-149344800	Weak transcription	Left Ventricle	heart
6	chr6:149321600-149336000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:149321600-149340600	Weak transcription	Aorta	Aorta
8	chr6:149321800-149332600	Weak transcription	HSMMtube	muscle
9	chr6:149321800-149335000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:149321800-149340200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:149321800-149349800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:149322600-149334400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:149323000-149333000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:149323000-149333000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:149323000-149334400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr6:149323000-149334600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr6:149323000-149335600	Weak transcription	Fetal Lung	lung
18	chr6:149323000-149342600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:149323600-149335600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:149323800-149333000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:149324600-149334600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr6:149325200-149333000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:149325800-149332600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:149326800-149332600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:149326800-149333000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:149327200-149331400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:149327200-149333200	Weak transcription	Lung	lung
28	chr6:149327200-149334200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr6:149327200-149334600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr6:149327200-149334800	Weak transcription	Fetal Stomach	stomach
31	chr6:149327200-149335200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr6:149327200-149340200	Weak transcription	Primary B cells from peripheral blood	blood
33	chr6:149327200-149340600	Weak transcription	Primary B cells from cord blood	blood
34	chr6:149327200-149353000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:149327400-149333000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:149327400-149334200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr6:149327400-149334800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr6:149327600-149335000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:149327600-149335800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:149327600-149342200	Weak transcription	Dnd41	blood
41	chr6:149328000-149335200	Weak transcription	Esophagus	oesophagus
42	chr6:149328600-149332800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:149328600-149335200	Weak transcription	Fetal Muscle Leg	muscle
44	chr6:149329400-149340600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr6:149329800-149332800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr6:149329800-149340200	Weak transcription	Ovary	ovary
47	chr6:149330000-149333000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr6:149330000-149333000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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