Variant report

Variant	rs2158395
Chromosome Location	chr11:17828930-17828931
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:17813467..17816316-chr11:17826867..17829141,2	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	0.82[ASN][1000 genomes]
rs11024415	0.81[CHB][hapmap]
rs11821847	0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1548528	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2107427	0.83[CEU][hapmap];0.81[CHB][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2237943	0.90[CHB][hapmap]
rs2237944	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2237946	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2237948	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2283248	0.98[ASN][1000 genomes]
rs2283249	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.98[ASN][1000 genomes]
rs2299630	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299632	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299633	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4757590	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4757591	0.81[CHB][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4757593	0.83[CEU][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes]
rs6486398	0.80[CHB][hapmap]
rs7106840	0.83[CEU][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7115183	0.81[CHB][hapmap]
rs718439	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs765989	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs7929668	0.81[CHB][hapmap]
rs7932686	0.83[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7935967	0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.86[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	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
rs2158395	SOX6	cis	cerebellum	SCAN
rs2158395	MRGPRX2	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17802800-17832400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr11:17805800-17829000	Weak transcription	Fetal Stomach	stomach
3	chr11:17806000-17837800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr11:17806800-17867400	Weak transcription	Primary B cells from cord blood	blood
5	chr11:17808200-17861400	Weak transcription	Thymus	Thymus
6	chr11:17808800-17834600	Weak transcription	Aorta	Aorta
7	chr11:17809000-17833200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:17810400-17829400	Weak transcription	Fetal Intestine Small	intestine
9	chr11:17811000-17830800	Weak transcription	Primary T cells from cord blood	blood
10	chr11:17815600-17841400	Weak transcription	HepG2	liver
11	chr11:17818600-17843200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr11:17820800-17832600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr11:17821200-17831800	Weak transcription	Esophagus	oesophagus
14	chr11:17824400-17830200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:17825400-17843400	Weak transcription	Lung	lung
16	chr11:17825600-17829000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:17825600-17832400	Weak transcription	Brain Substantia Nigra	brain
18	chr11:17825800-17829200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:17825800-17832000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr11:17826000-17832400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr11:17826600-17829200	Enhancers	Left Ventricle	heart
22	chr11:17826600-17832200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr11:17826800-17829400	Enhancers	Right Atrium	heart
24	chr11:17826800-17829600	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr11:17827000-17829600	Enhancers	Fetal Heart	heart
26	chr11:17827200-17829000	Weak transcription	Gastric	stomach
27	chr11:17827200-17829400	Enhancers	HSMMtube	muscle
28	chr11:17827400-17829800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr11:17827600-17829600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:17827800-17829400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:17827800-17829800	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr11:17828000-17829400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr11:17828200-17829600	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr11:17828200-17829600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr11:17828200-17831400	Weak transcription	Psoas Muscle	Psoas
36	chr11:17828400-17829000	Enhancers	Fetal Brain Male	brain
37	chr11:17828400-17829200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:17828400-17829200	Enhancers	Brain Anterior Caudate	brain
39	chr11:17828400-17829200	Enhancers	HSMM	muscle
40	chr11:17828400-17831600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr11:17828600-17829200	Enhancers	Brain Hippocampus Middle	brain
42	chr11:17828600-17829200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr11:17828600-17829400	Enhancers	Right Ventricle	heart
44	chr11:17828600-17829600	Enhancers	Fetal Brain Female	brain
45	chr11:17828800-17829200	Enhancers	Fetal Muscle Trunk	muscle
46	chr11:17828800-17829200	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr11:17828800-17829400	Enhancers	Brain Germinal Matrix	brain
48	chr11:17828800-17831600	Weak transcription	Fetal Muscle Leg	muscle

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