Variant report

Variant	rs7541850
Chromosome Location	chr1:84958166-84958167
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	chr1:84955760..84959867-chr1:84969764..84972842,4	MCF-7	breast:
2	chr1:84942484..84947798-chr1:84954955..84960241,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122432	Chromatin interaction
ENSG00000174021	Chromatin interaction
ENSG00000117133	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10493754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10874449	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11163973	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11163974	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11163975	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11163976	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11163982	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11163985	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11163986	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11163987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11163993	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11164001	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12075532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13093	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17110164	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17110485	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17110590	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1891126	1.00[CHB][hapmap]
rs3768247	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56876287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6576712	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs6658034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6658974	0.92[ASN][1000 genomes]
rs6660306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6662644	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6662683	0.92[ASN][1000 genomes]
rs6666052	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];0.84[ASN][1000 genomes]
rs6666572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6668752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6669593	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6676502	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6684882	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]
rs6688208	1.00[JPT][hapmap]
rs6690906	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6698596	1.00[CHB][hapmap]
rs6701280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6704452	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72948416	0.81[ASN][1000 genomes]
rs7524576	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];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7539413	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];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7541909	0.92[ASN][1000 genomes]
rs7547208	0.92[ASN][1000 genomes]
rs7551329	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7554311	1.00[CHB][hapmap]
rs7555773	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7555821	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];1.00[EUR][1000 genomes];0.92[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	chr1:84946000-84965800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:84946000-84967000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:84946000-84969600	Weak transcription	Esophagus	oesophagus
4	chr1:84946000-84970400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:84946000-84970800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:84946200-84962800	Weak transcription	HSMMtube	muscle
7	chr1:84946400-84962000	Weak transcription	Fetal Brain Male	brain
8	chr1:84946400-84962800	Weak transcription	Stomach Mucosa	stomach
9	chr1:84946800-84967400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:84947000-84965800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:84947200-84958400	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:84947400-84969800	Weak transcription	Aorta	Aorta
13	chr1:84947800-84966000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:84947800-84967800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:84949600-84968400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:84949800-84962000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:84951200-84971000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:84952400-84967400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:84953800-84968400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:84954000-84965800	Strong transcription	Dnd41	blood
21	chr1:84954400-84958600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:84954400-84963200	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:84954800-84959200	Strong transcription	NHEK	skin
24	chr1:84954800-84963400	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr1:84954800-84965800	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr1:84954800-84966400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr1:84954800-84966800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:84954800-84967000	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr1:84954800-84967600	Strong transcription	Primary hematopoietic stem cells	blood
30	chr1:84954800-84969200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:84955000-84959400	Strong transcription	Placenta	Placenta
32	chr1:84955000-84960000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:84955000-84960000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr1:84955000-84960000	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr1:84955000-84960200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:84955000-84960400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:84955000-84963400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr1:84955000-84963400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:84955000-84963600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr1:84955000-84963800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:84955000-84964200	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:84955000-84964800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:84955000-84965600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:84955000-84965800	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:84955000-84965800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:84955000-84966600	Strong transcription	Fetal Intestine Large	intestine
47	chr1:84955000-84966800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:84955000-84967000	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr1:84955000-84967200	Strong transcription	Fetal Thymus	thymus
50	chr1:84955000-84967200	Strong transcription	HSMM	muscle

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