Variant report

Variant	rs11916690
Chromosome Location	chr3:113012343-113012344
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	chr3:113005964..113007970-chr3:113009934..113012808,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11921931	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13064411	0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[ASN][1000 genomes]
rs13065651	0.91[ASN][1000 genomes]
rs13068107	0.96[ASN][1000 genomes]
rs13083453	0.83[ASN][1000 genomes]
rs13086266	0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs13325046	0.94[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1386336	0.94[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs1486894	0.88[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs16860849	0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[ASN][1000 genomes]
rs2018912	0.91[ASN][1000 genomes]
rs2087129	0.94[CEU][hapmap]
rs2129434	0.94[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs2291905	0.84[CEU][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs28536176	0.81[EUR][1000 genomes]
rs28710051	0.81[EUR][1000 genomes]
rs34049435	0.83[ASN][1000 genomes]
rs34056827	0.91[ASN][1000 genomes]
rs34680203	0.91[ASN][1000 genomes]
rs35765657	0.91[ASN][1000 genomes]
rs36108475	0.96[ASN][1000 genomes]
rs3732809	0.91[ASN][1000 genomes]
rs3773697	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.98[ASN][1000 genomes]
rs3829889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55693215	0.91[ASN][1000 genomes]
rs60131925	0.96[ASN][1000 genomes]
rs60279293	0.83[ASN][1000 genomes]
rs61366244	0.91[ASN][1000 genomes]
rs6773497	0.88[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs6783965	0.88[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs6786974	0.88[CEU][hapmap]
rs6787026	0.94[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs6808394	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs7610638	0.81[EUR][1000 genomes]
rs7619913	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs775231	1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs808950	0.81[TSI][hapmap]
rs9836396	0.94[CEU][hapmap]
rs9860549	0.94[CEU][hapmap]
rs9869119	0.81[EUR][1000 genomes]
rs9869318	0.94[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers 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 target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11916690	BOC	cis	parietal	SCAN
rs11916690	BOC	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:112990400-113036000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:112993800-113036000	Weak transcription	Right Ventricle	heart
4	chr3:112995200-113016000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:112995200-113022400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:112995400-113024000	Weak transcription	Aorta	Aorta
7	chr3:112995400-113035800	Weak transcription	Lung	lung
8	chr3:112995800-113013000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:112995800-113035800	Weak transcription	Thymus	Thymus
10	chr3:112996000-113025400	Weak transcription	Small Intestine	intestine
11	chr3:112996200-113034400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:112996400-113046400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:112997200-113036200	Weak transcription	Spleen	Spleen
14	chr3:112998600-113036000	Weak transcription	Gastric	stomach
15	chr3:113000200-113016400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:113000800-113014400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:113001200-113025400	Weak transcription	Brain Anterior Caudate	brain
18	chr3:113001200-113044600	Weak transcription	Fetal Kidney	kidney
19	chr3:113003200-113015400	Weak transcription	Brain Germinal Matrix	brain
20	chr3:113003400-113022600	Weak transcription	Colonic Mucosa	Colon
21	chr3:113003800-113016200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:113003800-113023000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:113004200-113023800	Weak transcription	Brain Substantia Nigra	brain
24	chr3:113004600-113016200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:113005600-113029800	Weak transcription	Fetal Intestine Large	intestine
26	chr3:113006200-113035400	Weak transcription	Esophagus	oesophagus
27	chr3:113006200-113036000	Weak transcription	Pancreas	Pancrea
28	chr3:113006600-113024000	Weak transcription	HSMMtube	muscle
29	chr3:113006800-113015800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:113006800-113022600	Weak transcription	Hela-S3	cervix
31	chr3:113006800-113031800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:113007000-113012400	Weak transcription	A549	lung
33	chr3:113007000-113016400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr3:113007000-113022000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:113007000-113022600	Weak transcription	Liver	Liver
36	chr3:113007000-113022800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:113007000-113023800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:113007000-113028000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:113007000-113034400	Weak transcription	HSMM	muscle
40	chr3:113007200-113043400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:113007600-113034200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr3:113008000-113014000	Weak transcription	Primary T cells from cord blood	blood
43	chr3:113008000-113023600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:113008200-113035800	Weak transcription	Fetal Intestine Small	intestine
45	chr3:113008400-113023800	Weak transcription	Fetal Muscle Leg	muscle
46	chr3:113008800-113016000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:113008800-113016000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:113009000-113032800	Weak transcription	Primary B cells from cord blood	blood
49	chr3:113009200-113013000	Weak transcription	Left Ventricle	heart
50	chr3:113010800-113015600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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