Variant report

Variant	rs4910075
Chromosome Location	chr11:9921549-9921550
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9918384..9921801-chr11:9925480..9929741,5	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10840315	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840323	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840325	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840327	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap]
rs10840337	1.00[CHB][hapmap]
rs10840338	1.00[CHB][hapmap]
rs11042486	1.00[CHB][hapmap]
rs11042500	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11042511	1.00[CHB][hapmap]
rs11042526	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042529	0.95[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042534	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042543	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042550	1.00[CHB][hapmap]
rs11042556	1.00[CHB][hapmap]
rs11042559	1.00[CHB][hapmap]
rs11042561	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap]
rs11042571	1.00[CHB][hapmap]
rs11042579	1.00[CHB][hapmap]
rs11042595	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap]
rs11042601	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap]
rs11042609	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap]
rs11042618	1.00[CHB][hapmap]
rs11042623	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap]
rs11601125	0.86[CEU][hapmap]
rs11601212	1.00[CHD][hapmap]
rs11602515	1.00[CHB][hapmap]
rs11603291	1.00[CHD][hapmap]
rs11607582	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417800	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12419564	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12419923	1.00[CHB][hapmap]
rs12420734	1.00[CHB][hapmap]
rs12421096	1.00[CHB][hapmap]
rs12421179	1.00[CHB][hapmap]
rs12421200	1.00[CHB][hapmap]
rs12421878	1.00[CHB][hapmap]
rs12786236	1.00[CHB][hapmap]
rs12808226	1.00[CHB][hapmap]
rs17268632	1.00[CHB][hapmap]
rs17269812	0.86[CEU][hapmap]
rs17270804	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17271847	1.00[CHB][hapmap]
rs17355675	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17355924	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17356792	1.00[CHB][hapmap]
rs4909915	1.00[CHB][hapmap]
rs4910077	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910080	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4910081	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.81[AFR][1000 genomes]
rs4910084	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4910497	1.00[CHB][hapmap]
rs4910505	1.00[CHB][hapmap]
rs61876937	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7115754	1.00[CHD][hapmap]
rs7131445	1.00[CHB][hapmap]
rs7928959	1.00[CHB][hapmap]
rs7938502	1.00[CHB][hapmap]
rs7938647	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.81[MEX][hapmap]
rs7943610	1.00[CHB][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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv2762895	chr11:9849511-9954549	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv896988	chr11:9912052-10012511	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4910075	PTH	cis	parietal	SCAN
rs4910075	OR10A5	cis	cerebellum	SCAN
rs4910075	OLFML1	cis	cerebellum	SCAN
rs4910075	SYT9	cis	cerebellum	SCAN
rs4910075	SCUBE2	cis	parietal	SCAN
rs4910075	NLRP14	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9878800-9952200	Weak transcription	Aorta	Aorta
2	chr11:9882400-9929600	Weak transcription	Primary T cells from cord blood	blood
3	chr11:9894400-9978600	Weak transcription	Left Ventricle	heart
4	chr11:9904000-9937000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr11:9910000-9954600	Weak transcription	Pancreas	Pancrea
6	chr11:9913600-9928800	Weak transcription	Right Ventricle	heart
7	chr11:9913800-9927400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:9914200-9926800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr11:9914400-9927600	Weak transcription	Brain Anterior Caudate	brain
10	chr11:9915000-9937200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr11:9915200-9922600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:9915400-9923200	Weak transcription	HSMMtube	muscle
13	chr11:9915400-9926800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr11:9915400-9927600	Weak transcription	Colon Smooth Muscle	Colon
15	chr11:9915600-9923400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr11:9915800-9923000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr11:9916600-9923000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr11:9916600-9925200	Weak transcription	Lung	lung
19	chr11:9916600-9932600	Weak transcription	Fetal Intestine Small	intestine
20	chr11:9916800-9921800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr11:9916800-9922800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr11:9916800-9923600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr11:9916800-9925000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr11:9916800-9944400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:9916800-9944400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr11:9917000-9923800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr11:9917000-9927600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr11:9917000-9937200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr11:9917200-9922800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr11:9917200-9923000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr11:9917200-9925000	Weak transcription	Ovary	ovary
32	chr11:9917200-9927400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:9917400-9921800	Weak transcription	Placenta	Placenta
34	chr11:9917400-9928000	Weak transcription	Brain Hippocampus Middle	brain
35	chr11:9917600-9922400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr11:9917600-9924000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr11:9917600-9927200	Weak transcription	Fetal Intestine Large	intestine
38	chr11:9917600-9927600	Weak transcription	Fetal Lung	lung
39	chr11:9917600-9928200	Weak transcription	Liver	Liver
40	chr11:9917600-9928200	Weak transcription	Fetal Heart	heart
41	chr11:9917600-9933200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr11:9917600-9934200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr11:9917600-9951800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr11:9917600-9952400	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr11:9917800-9926400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr11:9917800-9927400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr11:9917800-9927400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr11:9917800-9927600	Weak transcription	Adipose Nuclei	Adipose
49	chr11:9917800-9933200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr11:9917800-9952600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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