Variant report

Variant	rs6682078
Chromosome Location	chr1:59123995-59123996
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:59119791..59121727-chr1:59123555..59125768,2	MCF-7	breast:
2	chr1:59123673..59126344-chr1:59132381..59135089,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TACSTD2-2	chr1:59120412-59124660	NONHSAT003510

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10489540	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207278	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11207284	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11207297	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11207299	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12062727	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070703	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12073211	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12078684	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12080369	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12082192	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12092264	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12562490	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12737926	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12742701	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323281	0.87[TSI][hapmap]
rs17117968	0.94[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17118041	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17118097	0.88[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1961787	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs232869	0.80[JPT][hapmap]
rs2760480	0.85[TSI][hapmap]
rs2897558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35180093	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4244016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4414067	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4483434	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4553223	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4612650	0.89[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4912361	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4912364	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912365	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912366	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912371	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4912375	0.88[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55677434	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55892958	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56398740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61292499	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6659809	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6664796	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6673162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003930	chr1:58930444-59157038	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6682078	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59102000-59130400	Weak transcription	Aorta	Aorta
2	chr1:59108200-59130400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:59110800-59125200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:59112800-59125600	Weak transcription	NHLF	lung
5	chr1:59114400-59130200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:59115000-59132800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:59115600-59124400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:59115600-59138400	Weak transcription	Small Intestine	intestine
9	chr1:59115800-59124800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr1:59115800-59125000	Weak transcription	Fetal Brain Female	brain
11	chr1:59115800-59129800	Weak transcription	Brain Germinal Matrix	brain
12	chr1:59116000-59129200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:59116000-59129200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:59116000-59151600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:59116400-59125200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr1:59116400-59137800	Weak transcription	Fetal Heart	heart
17	chr1:59116800-59131400	Weak transcription	Fetal Stomach	stomach
18	chr1:59117000-59125200	Weak transcription	Fetal Kidney	kidney
19	chr1:59117800-59147600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:59118000-59139000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:59118200-59127200	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:59118200-59130400	Weak transcription	Brain Anterior Caudate	brain
23	chr1:59118200-59163400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:59118400-59125400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr1:59118400-59129600	Weak transcription	Fetal Brain Male	brain
26	chr1:59118400-59129600	Weak transcription	Stomach Mucosa	stomach
27	chr1:59118400-59130000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:59118600-59147400	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:59118800-59130200	Weak transcription	Brain Angular Gyrus	brain
30	chr1:59118800-59130400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:59119000-59135200	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr1:59119200-59130400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:59119800-59147600	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:59119800-59155000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:59119800-59162200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:59119800-59163200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:59120000-59143000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:59120000-59153400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:59120200-59149400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:59121000-59161200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:59121200-59130400	Strong transcription	Adipose Nuclei	Adipose
42	chr1:59121200-59141600	Strong transcription	Primary B cells from cord blood	blood
43	chr1:59121400-59124400	Strong transcription	Primary hematopoietic stem cells	blood
44	chr1:59121400-59134800	Strong transcription	Placenta	Placenta
45	chr1:59121400-59145400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:59121400-59161000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:59121600-59124000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr1:59121600-59124000	Strong transcription	Fetal Intestine Large	intestine
49	chr1:59121600-59124000	Strong transcription	Fetal Muscle Leg	muscle
50	chr1:59121600-59124000	Strong transcription	Spleen	Spleen

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