Variant report

Variant	rs9368878
Chromosome Location	chr6:35585614-35585615
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:35584531..35587499-chr6:35594692..35597176,2	K562	blood:
2	chr6:35576934..35581038-chr6:35582610..35587021,4	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12055438	0.81[EUR][1000 genomes]
rs1360780	0.88[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs1591365	1.00[EUR][1000 genomes]
rs2395634	0.84[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3798347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3800372	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3800373	0.94[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.85[YRI][hapmap];0.85[EUR][1000 genomes]
rs4713904	0.81[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.88[TSI][hapmap]
rs6902124	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6929873	0.84[ASN][1000 genomes]
rs6931118	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7751598	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9296158	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9296159	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9357201	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9357202	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9368881	0.85[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9368885	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9380522	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9380525	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9380526	0.85[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9394309	0.90[GIH][hapmap];0.88[TSI][hapmap]
rs943297	0.86[GIH][hapmap];0.83[TSI][hapmap]
rs9470080	0.81[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758048	chr6:35463741-35806504	Genic enhancers Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759420	chr6:35463741-35806504	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv462913	chr6:35502202-35592744	Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv602923	chr6:35502202-35592744	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv517211	chr6:35502202-35607571	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv602924	chr6:35505311-35750299	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv885801	chr6:35537406-35671651	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv3430300	chr6:35549151-35959004	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9368878	ANKS1A	cis	cerebellum	SCAN
rs9368878	HMGA1	cis	cerebellum	SCAN
rs9368878	FKBP5	Cis_1M	lymphoblastoid	RTeQTL
rs9368878	BRPF3	cis	cerebellum	SCAN
rs9368878	MDGA1	cis	cerebellum	SCAN
rs9368878	BAK1	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35545000-35601800	Weak transcription	Fetal Intestine Small	intestine
2	chr6:35569400-35591600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:35569600-35587800	Weak transcription	Placenta	Placenta
4	chr6:35570200-35608600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:35570600-35587800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:35570800-35586000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:35570800-35586200	Weak transcription	Fetal Stomach	stomach
8	chr6:35570800-35586200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:35570800-35611400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr6:35571000-35590600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr6:35571000-35602400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr6:35571200-35587200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr6:35571200-35611800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr6:35571400-35587200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:35572200-35586000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr6:35574000-35588800	Weak transcription	NH-A	brain
17	chr6:35574400-35587200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:35574800-35607200	Weak transcription	Hela-S3	cervix
19	chr6:35575000-35611600	Strong transcription	Liver	Liver
20	chr6:35575200-35592800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:35575600-35610400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:35575800-35587200	Weak transcription	Colonic Mucosa	Colon
23	chr6:35576200-35588000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:35576400-35589600	Strong transcription	Thymus	Thymus
25	chr6:35576800-35586000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
26	chr6:35576800-35587600	Weak transcription	Right Ventricle	heart
27	chr6:35577000-35592800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:35577400-35592800	Strong transcription	HSMM	muscle
29	chr6:35577400-35593000	Strong transcription	Fetal Thymus	thymus
30	chr6:35577400-35595200	Strong transcription	Left Ventricle	heart
31	chr6:35577600-35613200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr6:35578600-35587000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr6:35578600-35588000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:35578600-35589600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:35578800-35588800	Strong transcription	K562	blood
36	chr6:35578800-35592000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:35578800-35592800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:35579200-35588000	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr6:35579200-35597200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr6:35579400-35586200	Weak transcription	Fetal Heart	heart
41	chr6:35579400-35601400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:35579400-35603000	Weak transcription	HSMMtube	muscle
43	chr6:35579400-35603600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr6:35579400-35603800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr6:35579600-35588000	Strong transcription	Brain Anterior Caudate	brain
46	chr6:35579600-35593000	Strong transcription	Stomach Smooth Muscle	stomach
47	chr6:35579600-35604000	Weak transcription	Osteobl	bone
48	chr6:35579800-35587800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:35579800-35592000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:35579800-35593400	Strong transcription	Muscle Satellite Cultured Cells	--

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