Variant report

Variant	rs10910966
Chromosome Location	chr1:172010608-172010609
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172010411..172012805-chr1:172411810..172414746,2	MCF-7	breast:
2	chr1:172010410..172011489-chr1:172368146..172369453,8	MCF-7	breast:
3	chr1:172010329..172011675-chr1:172398087..172399170,9	MCF-7	breast:
4	chr1:172009534..172012040-chr1:172017929..172019999,2	MCF-7	breast:
5	chr1:172008308..172011065-chr1:172384057..172386802,2	MCF-7	breast:
6	chr1:171971691..171972193-chr1:172010147..172011060,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135845	Chromatin interaction
ENSG00000180999	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10157345	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10218612	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10218805	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10489730	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10797716	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10797719	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10797720	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10797725	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10797734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10797735	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10910939	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10910968	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10910969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10910970	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911109	0.94[JPT][hapmap]
rs10911112	0.94[JPT][hapmap]
rs10911121	0.81[JPT][hapmap]
rs12027295	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12028055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12037831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038713	0.99[ASN][1000 genomes]
rs12047492	0.88[JPT][hapmap]
rs12120556	0.94[JPT][hapmap]
rs12128720	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1555382	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1555383	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2038481	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2057302	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs2057303	0.81[ASN][1000 genomes]
rs2181624	0.94[JPT][hapmap]
rs2208367	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2295610	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs2295611	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs2421950	0.94[ASW][hapmap];0.98[LWK][hapmap];0.85[MKK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes]
rs36180993	0.81[ASN][1000 genomes]
rs3736791	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4076678	1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs4333881	0.81[ASN][1000 genomes]
rs4399191	0.87[AFR][1000 genomes]
rs4916241	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4916413	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs57907095	0.87[AFR][1000 genomes]
rs59316397	0.85[AFR][1000 genomes]
rs6413836	0.81[EUR][1000 genomes]
rs6425599	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6668552	0.83[AFR][1000 genomes]
rs6669406	0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6683503	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6700538	0.81[ASN][1000 genomes]
rs73037351	0.87[AFR][1000 genomes]
rs7518865	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7519236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7520595	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530970	0.80[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7533694	0.81[ASN][1000 genomes]
rs9286842	0.94[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];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][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	nsv532342	chr1:171922237-172133785	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
2	nsv3532	chr1:171997451-172042351	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171994000-172020400	Weak transcription	Left Ventricle	heart
2	chr1:172000000-172012800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:172000600-172013600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:172000800-172011400	Weak transcription	Right Ventricle	heart
5	chr1:172000800-172013800	Weak transcription	Fetal Brain Female	brain
6	chr1:172001400-172019000	Weak transcription	Fetal Brain Male	brain
7	chr1:172002200-172011600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:172002800-172013200	Weak transcription	Primary T cells from cord blood	blood
9	chr1:172003000-172012400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:172004000-172014000	Weak transcription	Lung	lung
11	chr1:172005600-172015200	Weak transcription	HSMMtube	muscle
12	chr1:172006000-172013800	Weak transcription	Brain Germinal Matrix	brain
13	chr1:172006400-172025600	Weak transcription	Adipose Nuclei	Adipose
14	chr1:172006800-172010800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:172007600-172014000	Weak transcription	Brain Substantia Nigra	brain
16	chr1:172007600-172014800	Weak transcription	Thymus	Thymus
17	chr1:172008200-172011000	Weak transcription	Ovary	ovary
18	chr1:172008400-172013200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:172008800-172010800	Enhancers	Hela-S3	cervix
20	chr1:172009000-172010800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:172009000-172010800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:172009000-172013800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:172009200-172010800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:172009200-172011600	Weak transcription	Fetal Kidney	kidney
25	chr1:172009200-172022800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:172009800-172010800	Strong transcription	Brain Angular Gyrus	brain
27	chr1:172009800-172010800	Strong transcription	Brain Anterior Caudate	brain
28	chr1:172010000-172022200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:172010200-172010800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:172010200-172011000	Weak transcription	Osteobl	bone
31	chr1:172010400-172010800	Enhancers	NHEK	skin
32	chr1:172010400-172011000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:172010400-172013800	Weak transcription	Brain Hippocampus Middle	brain
34	chr1:172010400-172014000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:172010400-172022000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:172010600-172011800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:172010600-172012800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr1:172010600-172014800	Weak transcription	Aorta	Aorta
39	chr1:172010600-172022400	Weak transcription	HMEC	breast
40	chr1:172010600-172051400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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