Variant report

Variant	rs6684882
Chromosome Location	chr1:84948165-84948166
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	chr1:84946525..84949349-chr1:84951021..84952787,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10493754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10874449	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11163973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11163974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11163975	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11163976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11163982	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163985	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163986	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11163987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163993	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11164001	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12075532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12354394	0.85[ASN][1000 genomes]
rs13093	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110164	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17110485	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17110590	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17110949	0.85[ASN][1000 genomes]
rs1891126	1.00[CHB][hapmap]
rs3768247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs56876287	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576712	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[ASN][1000 genomes]
rs6576714	0.82[ASN][1000 genomes]
rs6658034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6658974	1.00[ASN][1000 genomes]
rs6660306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6662644	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662683	1.00[ASN][1000 genomes]
rs6666052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6666572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6668752	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6669593	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6676502	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6688208	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6690906	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6698596	1.00[CHB][hapmap]
rs6701280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704452	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72948416	0.88[ASN][1000 genomes]
rs7524576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532298	0.82[ASN][1000 genomes]
rs7539413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7541909	1.00[ASN][1000 genomes]
rs7547208	1.00[ASN][1000 genomes]
rs7551329	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7554311	1.00[CHB][hapmap]
rs7555773	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84945600-84949000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:84946000-84948600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr1:84946000-84949000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:84946000-84949000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:84946000-84956400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:84946000-84956400	Weak transcription	Gastric	stomach
7	chr1:84946000-84956400	Weak transcription	Spleen	Spleen
8	chr1:84946000-84965800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:84946000-84967000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:84946000-84969600	Weak transcription	Esophagus	oesophagus
11	chr1:84946000-84970400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:84946000-84970800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:84946200-84948600	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr1:84946200-84948600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:84946200-84949000	Weak transcription	Fetal Stomach	stomach
16	chr1:84946200-84949200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:84946200-84955200	Weak transcription	Right Ventricle	heart
18	chr1:84946200-84956200	Weak transcription	Colonic Mucosa	Colon
19	chr1:84946200-84962800	Weak transcription	HSMMtube	muscle
20	chr1:84946400-84948200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:84946400-84948600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:84946400-84948600	Weak transcription	Osteobl	bone
23	chr1:84946400-84948800	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr1:84946400-84949000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:84946400-84949400	Weak transcription	NH-A	brain
26	chr1:84946400-84955200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:84946400-84955600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:84946400-84956200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:84946400-84956400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr1:84946400-84962000	Weak transcription	Fetal Brain Male	brain
31	chr1:84946400-84962800	Weak transcription	Stomach Mucosa	stomach
32	chr1:84946600-84948200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:84946600-84948200	Enhancers	Pancreatic Islets	Pancreatic Islet
34	chr1:84946600-84948600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:84946600-84950800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:84946600-84955600	Weak transcription	Brain Germinal Matrix	brain
37	chr1:84946600-84956400	Weak transcription	Psoas Muscle	Psoas
38	chr1:84946800-84948400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr1:84946800-84948600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
40	chr1:84946800-84955400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:84946800-84967400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:84947000-84948200	Genic enhancers	Duodenum Smooth Muscle	Duodenum
43	chr1:84947000-84948400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
44	chr1:84947000-84948400	Genic enhancers	Monocytes-CD14+_RO01746	blood
45	chr1:84947000-84948800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr1:84947000-84950400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:84947000-84950400	Strong transcription	Placenta	Placenta
48	chr1:84947000-84953200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:84947000-84965800	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:84947200-84948600	Weak transcription	Liver	Liver

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