Variant report

Variant	rs2237950
Chromosome Location	chr11:17831667-17831668
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:17823576..17826889-chr11:17829759..17833137,3	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1005008	0.90[EUR][1000 genomes]
rs10160556	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10766440	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832860	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1236206	0.96[ASN][1000 genomes]
rs1548528	0.84[CEU][hapmap];0.91[EUR][1000 genomes]
rs2079227	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2158396	0.83[EUR][1000 genomes]
rs2237943	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs2237944	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs2237946	0.92[CEU][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs2237948	0.92[CEU][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs2237952	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2283250	0.92[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs2283251	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2299634	1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs3802969	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3802970	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs4757589	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6486398	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs6486399	0.81[GIH][hapmap]
rs7110010	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs718439	0.92[CEU][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs765989	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs999420	0.88[ASN][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	nsv832078	chr11:17780503-17953521	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv1043973	chr11:17781560-17869896	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv897026	chr11:17823296-18084878	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2237950	SOX6	cis	cerebellum	SCAN
rs2237950	HBD	trans	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17802800-17832400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr11:17806000-17837800	Weak transcription	Primary B cells from peripheral blood	blood
3	chr11:17806800-17867400	Weak transcription	Primary B cells from cord blood	blood
4	chr11:17808200-17861400	Weak transcription	Thymus	Thymus
5	chr11:17808800-17834600	Weak transcription	Aorta	Aorta
6	chr11:17809000-17833200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:17815600-17841400	Weak transcription	HepG2	liver
8	chr11:17818600-17843200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr11:17820800-17832600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr11:17821200-17831800	Weak transcription	Esophagus	oesophagus
11	chr11:17825400-17843400	Weak transcription	Lung	lung
12	chr11:17825600-17832400	Weak transcription	Brain Substantia Nigra	brain
13	chr11:17825800-17832000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr11:17826000-17832400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr11:17826600-17832200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:17829000-17832400	Weak transcription	Fetal Brain Male	brain
17	chr11:17829200-17831800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr11:17829200-17831800	Weak transcription	Left Ventricle	heart
19	chr11:17829200-17832000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:17829200-17832200	Weak transcription	Fetal Stomach	stomach
21	chr11:17829200-17832400	Weak transcription	Brain Anterior Caudate	brain
22	chr11:17829200-17833400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr11:17829400-17832200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr11:17829400-17832200	Weak transcription	Brain Angular Gyrus	brain
25	chr11:17829400-17833400	Weak transcription	Gastric	stomach
26	chr11:17829400-17833600	Weak transcription	Fetal Intestine Large	intestine
27	chr11:17829600-17831800	Weak transcription	Fetal Heart	heart
28	chr11:17829600-17832400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr11:17829600-17832600	Weak transcription	Fetal Brain Female	brain
30	chr11:17829800-17832000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr11:17829800-17832200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr11:17829800-17833400	Weak transcription	Fetal Intestine Small	intestine
33	chr11:17831000-17836200	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr11:17831200-17834400	Enhancers	Brain Hippocampus Middle	brain
35	chr11:17831200-17837000	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr11:17831200-17849400	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr11:17831400-17832000	Enhancers	Psoas Muscle	Psoas
38	chr11:17831400-17833000	Enhancers	HSMMtube	muscle
39	chr11:17831400-17834400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr11:17831600-17831800	Weak transcription	Primary T cells from cord blood	blood
41	chr11:17831600-17831800	Enhancers	Pancreas	Pancrea
42	chr11:17831600-17832000	Enhancers	Adipose Nuclei	Adipose
43	chr11:17831600-17832600	Enhancers	Right Ventricle	heart
44	chr11:17831600-17833200	Enhancers	Right Atrium	heart
45	chr11:17831600-17834000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr11:17831600-17835600	Enhancers	Fetal Muscle Leg	muscle
47	chr11:17831600-17836400	Enhancers	Skeletal Muscle Female	skeletal muscle

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