Variant report

Variant	rs12200454
Chromosome Location	chr6:11495324-11495325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:11093559..11095482-chr6:11495067..11496598,2	MCF-7	breast:
2	chr6:11224747..11226720-chr6:11494534..11496251,2	MCF-7	breast:
3	chr6:11229014..11231620-chr6:11494391..11496101,2	MCF-7	breast:
4	chr6:11232197..11234142-chr6:11494778..11496668,2	MCF-7	breast:
5	chr6:11390303..11392933-chr6:11494450..11496978,4	MCF-7	breast:
6	chr6:11433709..11436638-chr6:11494109..11496934,3	MCF-7	breast:
7	chr6:11489653..11491693-chr6:11494680..11496394,2	MCF-7	breast:
8	chr6:11356223..11359281-chr6:11494815..11498233,5	MCF-7	breast:
9	chr6:11230707..11237186-chr6:11493072..11498269,11	MCF-7	breast:
10	chr6:11143454..11145339-chr6:11495146..11498003,3	MCF-7	breast:
11	chr6:11142754..11146580-chr6:11494452..11498982,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000224531	Chromatin interaction
ENSG00000111859	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10807114	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10807115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947398	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11751884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11752836	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11755780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11756371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12192094	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194771	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12198765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198774	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198950	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12200391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528839	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs145176	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1923525	0.89[ASN][1000 genomes]
rs2025184	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025185	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758307	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2807964	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs295051	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3857556	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4711306	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713593	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713594	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713618	0.80[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs480684	0.88[ASN][1000 genomes]
rs486127	0.86[ASN][1000 genomes]
rs487729	0.88[ASN][1000 genomes]
rs490327	0.90[ASN][1000 genomes]
rs493183	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs505685	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs505839	0.87[ASN][1000 genomes]
rs518183	0.86[ASN][1000 genomes]
rs528012	0.88[ASN][1000 genomes]
rs528087	0.88[ASN][1000 genomes]
rs533319	0.89[ASN][1000 genomes]
rs562508	0.89[ASN][1000 genomes]
rs568867	0.88[ASN][1000 genomes]
rs570714	0.88[ASN][1000 genomes]
rs575164	0.88[ASN][1000 genomes]
rs586117	0.82[ASN][1000 genomes]
rs588062	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs588948	0.88[ASN][1000 genomes]
rs594164	0.80[ASN][1000 genomes]
rs595877	0.95[CHB][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap];0.81[ASN][1000 genomes]
rs601505	0.89[ASN][1000 genomes]
rs609135	0.88[ASN][1000 genomes]
rs61570488	0.81[AMR][1000 genomes]
rs616729	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs617157	0.88[ASN][1000 genomes]
rs618573	0.86[ASN][1000 genomes]
rs618998	0.89[ASN][1000 genomes]
rs620867	0.88[ASN][1000 genomes]
rs623024	0.88[ASN][1000 genomes]
rs651001	0.84[ASN][1000 genomes]
rs671048	0.89[ASN][1000 genomes]
rs681483	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6899820	0.81[ASN][1000 genomes]
rs6901328	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6907796	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908807	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6913697	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6914208	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6914420	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6915153	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6915366	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6916089	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6930371	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6932324	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6940859	0.81[AMR][1000 genomes]
rs6941011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6941700	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7770004	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9348892	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9348895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348896	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366806	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394102	0.88[CEU][hapmap];0.91[JPT][hapmap]
rs9394117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394123	0.89[ASN][1000 genomes]
rs9394146	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9394154	0.95[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]

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	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv432848	chr6:11371614-11560114	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12200454	TMEM170B	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11486800-11496000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:11486800-11496800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:11487400-11495800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:11487400-11495800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr6:11491800-11495800	Weak transcription	Fetal Kidney	kidney
6	chr6:11491800-11497200	Enhancers	Primary B cells from peripheral blood	blood
7	chr6:11492000-11496200	Enhancers	Primary B cells from cord blood	blood
8	chr6:11492000-11498200	Enhancers	A549	lung
9	chr6:11492200-11497400	Enhancers	HepG2	liver
10	chr6:11492800-11496000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:11493000-11499800	Weak transcription	NH-A	brain
12	chr6:11493200-11496000	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr6:11493400-11496200	Weak transcription	Osteobl	bone
14	chr6:11493400-11497600	Enhancers	Placenta Amnion	Placenta Amnion
15	chr6:11493400-11498200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:11493600-11495800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:11493600-11496400	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr6:11493600-11496800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:11494200-11496400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:11494200-11498200	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr6:11494400-11500600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:11494600-11496000	Enhancers	Lung	lung
23	chr6:11494600-11496000	Flanking Active TSS	GM12878-XiMat	blood
24	chr6:11494600-11496600	Enhancers	Fetal Heart	heart
25	chr6:11494600-11497200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr6:11494800-11495400	Enhancers	Right Atrium	heart
27	chr6:11494800-11495600	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr6:11494800-11495800	Enhancers	Right Ventricle	heart
29	chr6:11494800-11496000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:11494800-11496400	Enhancers	Fetal Stomach	stomach
31	chr6:11494800-11496600	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr6:11495000-11495400	Enhancers	Placenta	Placenta
33	chr6:11495000-11495600	Weak transcription	Spleen	Spleen
34	chr6:11495000-11496000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:11495000-11496000	Enhancers	Left Ventricle	heart
36	chr6:11495000-11497000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:11495000-11497200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:11495200-11495400	Enhancers	Brain Anterior Caudate	brain
39	chr6:11495200-11495400	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr6:11495200-11496200	Weak transcription	Brain Hippocampus Middle	brain
41	chr6:11495200-11496200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr6:11495200-11496400	Enhancers	Brain Angular Gyrus	brain

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