Variant report

Variant	rs12193567
Chromosome Location	chr6:53721818-53721819
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53719967..53722619-chr6:53723859..53726928,3	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10948783	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10948784	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12194768	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12209621	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3935664	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4128619	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4236114	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4260754	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4265034	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4273680	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4331986	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4392712	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4583974	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4612163	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4624872	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4645423	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6458967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458968	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6904545	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6906921	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6907027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6910777	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6913431	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6935621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6935838	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7453639	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745548	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7749635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7749749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751036	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7755924	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7761285	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9296722	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9296723	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9349682	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9349683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349684	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9367543	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9370234	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9370237	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9370238	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9370240	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9382240	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9382242	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9382243	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs9382244	0.80[ASN][1000 genomes]
rs9382245	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9382247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382254	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs9395879	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9395880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9395881	0.80[ASN][1000 genomes]
rs9395882	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9395883	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9395884	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9395887	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12193567	ELOVL5	cis	parietal	SCAN
rs12193567	LRRC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:53703200-53726400	Weak transcription	Fetal Stomach	stomach
3	chr6:53703800-53727600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:53706000-53722400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:53706200-53722000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
7	chr6:53713000-53722000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:53717800-53731800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:53718400-53723400	Enhancers	Stomach Mucosa	stomach
10	chr6:53718800-53723400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:53719800-53722000	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr6:53719800-53727600	Enhancers	Brain Substantia Nigra	brain
13	chr6:53719800-53727800	Enhancers	Brain Hippocampus Middle	brain
14	chr6:53719800-53747800	Weak transcription	Primary T cells from cord blood	blood
15	chr6:53720000-53722600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr6:53720000-53723000	Enhancers	Left Ventricle	heart
17	chr6:53720000-53724000	Enhancers	Brain Cingulate Gyrus	brain
18	chr6:53720000-53724400	Enhancers	Brain Anterior Caudate	brain
19	chr6:53720000-53727600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:53720200-53722200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr6:53720200-53722400	Enhancers	Brain Angular Gyrus	brain
22	chr6:53720200-53722600	Weak transcription	Colon Smooth Muscle	Colon
23	chr6:53720200-53723000	Enhancers	Right Atrium	heart
24	chr6:53720200-53723000	Enhancers	Right Ventricle	heart
25	chr6:53720400-53722800	Enhancers	HepG2	liver
26	chr6:53720400-53723000	Enhancers	Gastric	stomach
27	chr6:53720600-53722000	Weak transcription	NHEK	skin
28	chr6:53720600-53722400	Weak transcription	Lung	lung
29	chr6:53720600-53741400	Weak transcription	Dnd41	blood
30	chr6:53720800-53736600	Weak transcription	Fetal Thymus	thymus
31	chr6:53721000-53722000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:53721000-53722000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:53721000-53723400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:53721200-53726200	Weak transcription	Fetal Intestine Small	intestine
35	chr6:53721200-53726400	Weak transcription	Fetal Intestine Large	intestine
36	chr6:53721200-53726600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr6:53721200-53726800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr6:53721400-53722000	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr6:53721400-53722400	Weak transcription	HSMMtube	muscle
40	chr6:53721400-53723000	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr6:53721400-53724200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:53721600-53722200	Enhancers	HUVEC	blood vessel
43	chr6:53721600-53722400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:53721600-53723200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:53721600-53723200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:53721600-53723400	Enhancers	Esophagus	oesophagus
47	chr6:53721600-53728000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:53721800-53722000	Enhancers	Brain Germinal Matrix	brain
49	chr6:53721800-53722200	Weak transcription	Pancreas	Pancrea
50	chr6:53721800-53722400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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