Variant report

Variant	rs6659261
Chromosome Location	chr1:184447469-184447470
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:184442540..184447165-chr1:184447352..184452325,7	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10399817	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs10911610	0.89[CHB][hapmap]
rs12117823	1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.97[ASN][1000 genomes]
rs12120604	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12121612	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs12127697	0.94[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs12129904	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs12138103	0.93[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs12141469	0.85[ASN][1000 genomes]
rs12143271	0.82[ASN][1000 genomes]
rs1535132	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs16823195	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16823197	1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.97[ASN][1000 genomes]
rs16823238	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2180072	0.85[ASN][1000 genomes]
rs2207526	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs2207527	0.95[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs35682339	0.81[ASN][1000 genomes]
rs58231072	0.97[ASN][1000 genomes]
rs61825202	0.85[ASN][1000 genomes]
rs61825204	0.82[ASN][1000 genomes]
rs61825205	0.82[ASN][1000 genomes]
rs6683932	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6693408	0.94[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.81[ASN][1000 genomes]
rs7513091	0.94[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs7525267	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7548188	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6659261	TDRD5	cis	parietal	SCAN
rs6659261	EDEM3	cis	parietal	SCAN
rs6659261	HMCN1	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184427400-184448400	Weak transcription	Fetal Muscle Leg	muscle
2	chr1:184429000-184454800	Weak transcription	Aorta	Aorta
3	chr1:184429400-184449600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:184430600-184449800	Weak transcription	Right Ventricle	heart
5	chr1:184430600-184450000	Weak transcription	Fetal Stomach	stomach
6	chr1:184431800-184447600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:184433600-184449600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:184438000-184450600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:184439200-184453600	Weak transcription	Fetal Brain Female	brain
10	chr1:184441000-184452000	Weak transcription	Colonic Mucosa	Colon
11	chr1:184442000-184448400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:184442800-184447800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:184442800-184449200	Weak transcription	Placenta	Placenta
14	chr1:184442800-184449600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:184444200-184449000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:184444200-184449800	Weak transcription	Ovary	ovary
17	chr1:184444200-184449800	Weak transcription	Right Atrium	heart
18	chr1:184444200-184450400	Weak transcription	Pancreas	Pancrea
19	chr1:184444200-184453400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr1:184444400-184447800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:184444400-184448000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:184444400-184450400	Weak transcription	NHDF-Ad	bronchial
23	chr1:184444400-184452000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:184444600-184449800	Weak transcription	Adipose Nuclei	Adipose
25	chr1:184444600-184452600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:184444600-184460400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:184444800-184450000	Weak transcription	Fetal Lung	lung
28	chr1:184444800-184450400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:184444800-184451600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:184444800-184452200	Weak transcription	Fetal Kidney	kidney
31	chr1:184445200-184448400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:184445400-184449000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:184445400-184449600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:184445600-184448800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:184445600-184449200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:184445600-184449400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:184445600-184449800	Weak transcription	Psoas Muscle	Psoas
38	chr1:184445800-184450200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:184446000-184447600	Strong transcription	Fetal Intestine Large	intestine
40	chr1:184446000-184447800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr1:184446200-184448200	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:184446400-184447600	Weak transcription	HMEC	breast
43	chr1:184446400-184448400	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:184446400-184449400	Strong transcription	Primary hematopoietic stem cells	blood
45	chr1:184446400-184450600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:184446400-184452000	Weak transcription	Osteobl	bone
47	chr1:184446600-184450000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:184446600-184450000	Weak transcription	Lung	lung
49	chr1:184446600-184450000	Weak transcription	NHEK	skin
50	chr1:184446600-184450000	Weak transcription	NHLF	lung

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