Variant report

Variant	rs7109505
Chromosome Location	chr11:36288752-36288753
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:36287261..36290028-chr11:36291712..36296063,4	MCF-7	breast:
2	chr11:35638958..35641103-chr11:36285912..36290081,3	MCF-7	breast:
3	chr11:36279871..36282445-chr11:36287760..36289832,2	K562	blood:

Variant related genes	Relation type
ENSG00000196559	Chromatin interaction
ENSG00000179431	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10836528	0.86[YRI][hapmap]
rs10836531	0.80[MKK][hapmap]
rs11033524	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11033527	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11602024	0.86[AFR][1000 genomes]
rs11603166	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12361221	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1562327	0.81[CEU][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs17814690	0.86[YRI][hapmap]
rs1900336	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2289986	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2289987	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4418777	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56386213	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs61878683	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs61878687	0.87[EUR][1000 genomes]
rs6484831	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7104737	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7107433	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72946165	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7951298	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9667667	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9787880	0.89[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];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9787894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9888212	0.95[EUR][1000 genomes]
rs9888261	0.96[CEU][hapmap];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467791	chr11:36108497-36999385	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv554003	chr11:36108497-36999385	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7109505	LINC00610	cis	Thyroid	GTEx
rs7109505	SLC1A2	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:36276800-36294400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:36278200-36292600	Weak transcription	Esophagus	oesophagus
3	chr11:36278200-36293200	Weak transcription	Fetal Lung	lung
4	chr11:36279200-36292000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:36279200-36294800	Weak transcription	HMEC	breast
6	chr11:36280400-36291200	Weak transcription	Brain Angular Gyrus	brain
7	chr11:36280400-36294800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr11:36280400-36299000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:36280800-36291200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr11:36280800-36291400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr11:36280800-36292000	Weak transcription	Brain Substantia Nigra	brain
12	chr11:36280800-36300200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:36281000-36292600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr11:36281400-36292200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:36281400-36293200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr11:36282000-36292000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr11:36282200-36302000	Weak transcription	NHEK	skin
18	chr11:36282800-36292200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:36283000-36291200	Weak transcription	Spleen	Spleen
20	chr11:36283000-36298000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr11:36283200-36300000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr11:36285000-36291000	Weak transcription	Fetal Intestine Small	intestine
23	chr11:36286400-36293000	Weak transcription	Right Ventricle	heart
24	chr11:36287000-36291000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:36287000-36294200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr11:36287400-36289000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:36287400-36290800	Enhancers	Liver	Liver
28	chr11:36287400-36291400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr11:36287600-36291000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr11:36287600-36291000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr11:36287600-36291800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr11:36287600-36295400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr11:36287600-36304800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr11:36287800-36289400	Enhancers	Pancreas	Pancrea
35	chr11:36287800-36290600	Weak transcription	Fetal Brain Female	brain
36	chr11:36287800-36291000	Weak transcription	Fetal Stomach	stomach
37	chr11:36287800-36291200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:36287800-36291200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr11:36287800-36291200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr11:36287800-36292000	Weak transcription	Brain Anterior Caudate	brain
41	chr11:36287800-36292000	Weak transcription	Brain Germinal Matrix	brain
42	chr11:36287800-36292200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr11:36287800-36292400	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr11:36287800-36292800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr11:36287800-36293400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr11:36288000-36291200	Weak transcription	Brain Hippocampus Middle	brain
47	chr11:36288000-36291200	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr11:36288000-36293200	Weak transcription	Osteobl	bone
49	chr11:36288000-36310200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr11:36288200-36291000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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