Variant report

Variant	rs2299921
Chromosome Location	chr14:78064979-78064980
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:78063987..78068208-chr14:78069326..78072935,4	MCF-7	breast:
2	chr14:78064657..78067063-chr14:78079647..78083000,3	MCF-7	breast:
3	chr14:78064498..78067393-chr14:78068632..78070407,3	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10129280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10139059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10139421	0.88[YRI][hapmap]
rs10140195	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs10146161	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10873309	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11626349	0.85[CHB][hapmap];0.95[CHD][hapmap]
rs12587835	0.80[ASN][1000 genomes]
rs12887526	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs176901	0.81[CHB][hapmap];0.93[CHD][hapmap]
rs1861942	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1990806	0.80[CHB][hapmap]
rs2267746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267747	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267748	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2267749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267750	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2267754	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2299920	0.81[CHD][hapmap]
rs2299922	0.81[CHB][hapmap];0.90[CHD][hapmap];0.80[ASN][1000 genomes]
rs2299923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299925	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299927	0.81[CHB][hapmap];0.91[CHD][hapmap]
rs2299928	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4899660	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4899661	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4903614	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58598324	0.80[ASN][1000 genomes]
rs7144314	0.85[CHD][hapmap]
rs7157356	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7158771	0.80[ASN][1000 genomes]
rs8008258	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8021376	0.94[ASN][1000 genomes]
rs8021660	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9944097	0.81[CHB][hapmap];0.88[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832835	chr14:77906706-78095207	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1053810	chr14:77987871-78148320	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1051554	chr14:78004196-78122980	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2299921	COQ6	cis	parietal	SCAN
rs2299921	NEK9	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78013200-78066200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:78021800-78068400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:78021800-78071600	Weak transcription	Colon Smooth Muscle	Colon
4	chr14:78042400-78066600	Weak transcription	Fetal Brain Female	brain
5	chr14:78047400-78070000	Weak transcription	Fetal Brain Male	brain
6	chr14:78048200-78067200	Weak transcription	Hela-S3	cervix
7	chr14:78049400-78066400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr14:78051400-78066200	Weak transcription	Pancreas	Pancrea
9	chr14:78051400-78070200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr14:78051600-78072600	Weak transcription	Psoas Muscle	Psoas
11	chr14:78055000-78081600	Weak transcription	Right Ventricle	heart
12	chr14:78056600-78072800	Weak transcription	Placenta	Placenta
13	chr14:78056800-78070000	Weak transcription	Gastric	stomach
14	chr14:78057000-78065000	Weak transcription	Lung	lung
15	chr14:78057400-78070000	Weak transcription	Spleen	Spleen
16	chr14:78057600-78081400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr14:78057800-78065000	Weak transcription	Small Intestine	intestine
18	chr14:78059000-78065800	Weak transcription	Colonic Mucosa	Colon
19	chr14:78060200-78066800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr14:78060200-78069400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr14:78060400-78065000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr14:78060400-78065400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr14:78060600-78065200	Weak transcription	Fetal Kidney	kidney
24	chr14:78061600-78070000	Weak transcription	Esophagus	oesophagus
25	chr14:78061800-78069800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr14:78062200-78066000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr14:78062200-78066200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr14:78062200-78068200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr14:78062200-78070200	Weak transcription	Ovary	ovary
30	chr14:78062600-78065000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr14:78062600-78065000	Weak transcription	HSMMtube	muscle
32	chr14:78062600-78066400	Weak transcription	Fetal Intestine Small	intestine
33	chr14:78062800-78075000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr14:78063200-78065000	Weak transcription	Thymus	Thymus
35	chr14:78063200-78070000	Weak transcription	Brain Germinal Matrix	brain
36	chr14:78063200-78077800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr14:78063400-78065000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr14:78063400-78065000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr14:78063400-78065000	Weak transcription	Brain Angular Gyrus	brain
40	chr14:78063400-78065000	Weak transcription	Left Ventricle	heart
41	chr14:78063400-78065000	Weak transcription	HMEC	breast
42	chr14:78063400-78069400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr14:78063400-78069400	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr14:78063400-78069800	Weak transcription	Liver	Liver
45	chr14:78063400-78070000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr14:78063400-78070200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr14:78063400-78070200	Weak transcription	Fetal Thymus	thymus
48	chr14:78063400-78081600	Weak transcription	Fetal Stomach	stomach
49	chr14:78063600-78065000	Weak transcription	Brain Anterior Caudate	brain
50	chr14:78063600-78065000	Weak transcription	NHDF-Ad	bronchial

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