Variant report

Variant	rs60845773
Chromosome Location	chr6:87974150-87974151
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	chr6:87861169..87862980-chr6:87971439..87974356,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188994	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10488045	0.94[EUR][1000 genomes]
rs10498960	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878570	0.88[EUR][1000 genomes]
rs16878622	0.88[EUR][1000 genomes]
rs16878638	0.88[EUR][1000 genomes]
rs16878712	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs16878713	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs16878729	0.91[EUR][1000 genomes]
rs16878734	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16878736	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16878809	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16878856	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878863	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878942	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878991	0.91[AFR][1000 genomes]
rs16878999	0.91[AFR][1000 genomes]
rs16879012	0.86[AFR][1000 genomes]
rs1925693	0.94[EUR][1000 genomes]
rs41273281	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41273283	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55647962	0.85[EUR][1000 genomes]
rs56193950	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56305030	0.91[AFR][1000 genomes]
rs56678817	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56743579	0.88[EUR][1000 genomes]
rs56847789	0.85[EUR][1000 genomes]
rs56999910	0.88[EUR][1000 genomes]
rs57043501	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57116567	0.88[EUR][1000 genomes]
rs57217108	0.88[EUR][1000 genomes]
rs57421283	0.94[EUR][1000 genomes]
rs57552196	0.91[AFR][1000 genomes]
rs57607342	0.88[EUR][1000 genomes]
rs57962992	0.85[EUR][1000 genomes]
rs58269367	0.94[EUR][1000 genomes]
rs58327183	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58474842	0.94[EUR][1000 genomes]
rs58731649	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58735749	0.94[EUR][1000 genomes]
rs58751410	0.85[EUR][1000 genomes]
rs59138817	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59150116	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59214037	0.94[EUR][1000 genomes]
rs59495279	0.88[EUR][1000 genomes]
rs59597706	0.86[AFR][1000 genomes]
rs59654654	0.87[EUR][1000 genomes]
rs59875769	0.94[EUR][1000 genomes]
rs60074363	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs60285195	0.94[EUR][1000 genomes]
rs60544317	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60628059	0.84[AFR][1000 genomes]
rs60985818	0.81[EUR][1000 genomes]
rs60994855	0.85[EUR][1000 genomes]
rs61047847	0.88[EUR][1000 genomes]
rs61174011	0.86[AFR][1000 genomes]
rs61379368	0.94[EUR][1000 genomes]
rs61705669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73483720	0.94[EUR][1000 genomes]
rs73483728	0.94[EUR][1000 genomes]
rs73483743	0.94[EUR][1000 genomes]
rs73483749	0.94[EUR][1000 genomes]
rs73483752	0.94[EUR][1000 genomes]
rs73483758	0.94[EUR][1000 genomes]
rs73483760	0.94[EUR][1000 genomes]
rs73483765	0.94[EUR][1000 genomes]
rs73483769	0.94[EUR][1000 genomes]
rs73483771	0.91[EUR][1000 genomes]
rs73483774	0.94[EUR][1000 genomes]
rs73483790	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73483796	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73483799	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73485808	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73485811	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73485813	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73485815	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73485820	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73485826	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73485828	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73485831	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73485848	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73485849	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73499800	0.88[EUR][1000 genomes]
rs73499802	0.88[EUR][1000 genomes]
rs73501611	0.85[EUR][1000 genomes]
rs73501620	0.88[EUR][1000 genomes]
rs73501623	0.88[EUR][1000 genomes]
rs73501629	0.88[EUR][1000 genomes]
rs73501632	0.88[EUR][1000 genomes]
rs73501636	0.88[EUR][1000 genomes]
rs73501638	0.88[EUR][1000 genomes]
rs73501641	0.88[EUR][1000 genomes]
rs73501658	0.88[EUR][1000 genomes]
rs73501662	0.88[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	esv2758067	chr6:87817883-87992957	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2759453	chr6:87817883-87992957	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87957200-87981000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:87966200-87977200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr6:87966400-87976400	Weak transcription	Brain Angular Gyrus	brain
4	chr6:87966400-87989200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:87967000-87976000	Weak transcription	Brain Hippocampus Middle	brain
6	chr6:87967600-87983000	Weak transcription	Esophagus	oesophagus
7	chr6:87967800-87989000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr6:87968000-87976200	Weak transcription	Fetal Stomach	stomach
9	chr6:87968200-87975000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:87968200-87975400	Weak transcription	Osteobl	bone
11	chr6:87968200-87975600	Weak transcription	Adipose Nuclei	Adipose
12	chr6:87968200-87976000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:87968200-87977200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:87968200-87991200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:87968400-87975000	Weak transcription	Fetal Muscle Leg	muscle
16	chr6:87968400-87976200	Weak transcription	HepG2	liver
17	chr6:87968400-87984400	Weak transcription	NHDF-Ad	bronchial
18	chr6:87968600-87984200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:87969800-87974800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:87969800-87981800	Weak transcription	Primary T cells from cord blood	blood
21	chr6:87970000-87976400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr6:87970000-87977600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr6:87970000-87984600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:87970200-87975600	Weak transcription	Fetal Lung	lung
25	chr6:87970200-87976200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr6:87970200-87976200	Weak transcription	GM12878-XiMat	blood
27	chr6:87970200-87976400	Weak transcription	Thymus	Thymus
28	chr6:87970200-87978000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr6:87970200-87984600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr6:87970400-87974600	Weak transcription	Placenta	Placenta
31	chr6:87970400-87975600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:87970400-87976400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr6:87970400-87978000	Weak transcription	Left Ventricle	heart
34	chr6:87970400-87984400	Weak transcription	NH-A	brain
35	chr6:87970600-87976400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:87970600-87976600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr6:87970600-87977200	Weak transcription	Fetal Kidney	kidney
38	chr6:87970600-87983400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:87970600-87984200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:87970600-87988800	Weak transcription	Fetal Thymus	thymus
41	chr6:87970600-87994800	Weak transcription	Fetal Brain Female	brain
42	chr6:87970800-87975200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr6:87970800-87975600	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr6:87970800-87975600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr6:87971200-87974400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:87971200-87976200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:87971200-87985800	Weak transcription	Brain Germinal Matrix	brain
48	chr6:87971400-87976400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr6:87971400-87977200	Weak transcription	HSMM	muscle
50	chr6:87971400-87977800	Weak transcription	Dnd41	blood

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