Variant report

Variant	rs9355581
Chromosome Location	chr6:166865273-166865274
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10806850	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10806851	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10806852	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10806853	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12153873	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12191994	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2072828	0.82[YRI][hapmap]
rs2281052	0.83[CEU][hapmap];0.94[LWK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs2294330	0.90[CEU][hapmap];0.89[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3752927	0.81[AFR][1000 genomes]
rs4710049	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4710050	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4710051	0.95[CEU][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6910121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6913835	0.90[EUR][1000 genomes]
rs6915132	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6932660	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6941841	0.83[EUR][1000 genomes]
rs73033724	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7739961	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7741232	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9295346	0.85[EUR][1000 genomes]
rs9355580	0.90[CEU][hapmap];0.89[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv886937	chr6:166830696-166922813	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv886938	chr6:166859725-166904398	Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv886939	chr6:166859725-166922813	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9355581	DACT2	cis	parietal	SCAN
rs9355581	UNC93A	cis	parietal	SCAN
rs9355581	PHF10	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166808200-166911800	Weak transcription	Psoas Muscle	Psoas
2	chr6:166824000-166901400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:166825200-166875800	Weak transcription	Colonic Mucosa	Colon
4	chr6:166827000-166873400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:166827600-166867200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr6:166830000-166866600	Weak transcription	Fetal Intestine Large	intestine
7	chr6:166833200-166879000	Weak transcription	NH-A	brain
8	chr6:166833400-166879000	Weak transcription	HSMM	muscle
9	chr6:166834000-166866400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:166834200-166879400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:166846000-166881000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:166850200-166870000	Weak transcription	Right Atrium	heart
13	chr6:166861400-166873800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:166862000-166871600	Weak transcription	HMEC	breast
15	chr6:166862200-166869400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:166862400-166871000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:166862400-166871000	Weak transcription	NHDF-Ad	bronchial
18	chr6:166862400-166873800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:166862400-166900600	Weak transcription	Primary T cells from cord blood	blood
20	chr6:166862400-166920600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:166862600-166867200	Weak transcription	Adipose Nuclei	Adipose
22	chr6:166862600-166870000	Weak transcription	Osteobl	bone
23	chr6:166862600-166870800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr6:166862600-166871600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:166862600-166878800	Weak transcription	Brain Substantia Nigra	brain
26	chr6:166862600-166879400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr6:166862600-166883000	Weak transcription	Aorta	Aorta
28	chr6:166862600-166883000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr6:166862800-166866000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:166862800-166869400	Weak transcription	Left Ventricle	heart
31	chr6:166862800-166870200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:166862800-166871600	Weak transcription	Liver	Liver
33	chr6:166862800-166873800	Weak transcription	Spleen	Spleen
34	chr6:166862800-166878000	Weak transcription	HSMMtube	muscle
35	chr6:166863200-166866800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr6:166863200-166867200	Weak transcription	Brain Hippocampus Middle	brain
37	chr6:166863200-166869000	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr6:166863400-166871000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:166863400-166876600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr6:166863600-166865400	Strong transcription	Lung	lung
41	chr6:166863600-166900200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:166863600-166902000	Weak transcription	Small Intestine	intestine
43	chr6:166864000-166869800	Weak transcription	Stomach Mucosa	stomach
44	chr6:166864000-166871000	Weak transcription	Primary B cells from cord blood	blood
45	chr6:166864200-166866800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:166864200-166871000	Weak transcription	Fetal Muscle Leg	muscle
47	chr6:166864200-166872600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr6:166864600-166865600	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr6:166864600-166867800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:166864600-166870600	Weak transcription	Muscle Satellite Cultured Cells	--

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