Variant report

Variant	rs1549788
Chromosome Location	chr7:128879378-128879379
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:128865235..128868002-chr7:128877453..128879844,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10215998	1.00[EUR][1000 genomes]
rs10235589	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10249336	0.81[AFR][1000 genomes]
rs10255583	0.87[AFR][1000 genomes]
rs10264209	0.87[AMR][1000 genomes]
rs10269495	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10281269	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12533108	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13240723	1.00[EUR][1000 genomes]
rs1405475	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1469554	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1526898	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1526899	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1609043	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1991645	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2052962	0.87[AMR][1000 genomes]
rs2402946	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2402947	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2463096	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2566875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2566881	1.00[EUR][1000 genomes]
rs2566882	1.00[EUR][1000 genomes]
rs2694570	0.81[AFR][1000 genomes]
rs2694575	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2694576	1.00[EUR][1000 genomes]
rs2694577	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2694583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2694591	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2718085	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2718090	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2718091	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2718092	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2718097	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2718100	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28399138	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28437865	0.87[AMR][1000 genomes]
rs28475451	0.87[AMR][1000 genomes]
rs28864519	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2896414	0.92[AFR][1000 genomes]
rs4731567	1.00[EUR][1000 genomes]
rs6467234	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6467236	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6467239	0.81[AFR][1000 genomes]
rs6949882	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6950279	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6950496	0.89[AFR][1000 genomes]
rs6970267	0.95[AFR][1000 genomes]
rs71529418	0.91[AFR][1000 genomes]
rs71577870	0.91[AFR][1000 genomes]
rs7805353	0.87[AMR][1000 genomes]
rs9641847	1.00[EUR][1000 genomes]
rs9641848	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv1031284	chr7:128866118-128910506	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128866000-128880000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:128866000-128902200	Weak transcription	Gastric	stomach
3	chr7:128866200-128898600	Weak transcription	Thymus	Thymus
4	chr7:128866400-128891400	Weak transcription	Fetal Stomach	stomach
5	chr7:128866400-128899000	Weak transcription	Ovary	ovary
6	chr7:128866600-128880200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr7:128866600-128880400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr7:128866600-128901400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:128866800-128889600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr7:128867000-128884200	Weak transcription	Primary T cells from cord blood	blood
11	chr7:128867000-128898400	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr7:128867200-128909800	Weak transcription	Primary B cells from cord blood	blood
13	chr7:128867600-128885600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr7:128867800-128880400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr7:128868400-128880000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr7:128868600-128897200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr7:128869000-128880000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr7:128869800-128880200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr7:128869800-128880200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr7:128871800-128880200	Weak transcription	Brain Hippocampus Middle	brain
21	chr7:128872800-128892000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr7:128873400-128880000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:128875200-128880200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr7:128876400-128889800	Weak transcription	Fetal Intestine Small	intestine
25	chr7:128876600-128882000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr7:128878800-128880200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr7:128878800-128881400	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr7:128878800-128897000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr7:128879200-128880200	Weak transcription	NHEK	skin

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