Variant report

Variant	rs28399138
Chromosome Location	chr7:128884807-128884808
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:128863037..128866889-chr7:128882617..128886190,4	MCF-7	breast:
2	chr7:128873646..128876213-chr7:128883173..128885864,2	K562	blood:
3	chr7:128877623..128879223-chr7:128884322..128886478,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SMO-1	chr7:128884633-128884891	expReg_chr7_10024_+

Variant related genes	Relation type
ENSG00000158467	Chromatin interaction

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

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

rs_ID	r²[population]
rs10215998	1.00[EUR][1000 genomes]
rs10235589	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10255583	0.85[AFR][1000 genomes]
rs10264209	0.87[AMR][1000 genomes]
rs10269495	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10281269	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12533108	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13240723	1.00[EUR][1000 genomes]
rs1405475	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1469554	1.00[EUR][1000 genomes]
rs1526898	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1526899	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1549788	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1609043	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1991645	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2052962	0.87[AMR][1000 genomes]
rs2402946	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2402947	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2463096	1.00[EUR][1000 genomes]
rs2566875	0.93[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	0.83[AFR][1000 genomes]
rs2694575	0.92[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	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2694591	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2718085	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2718090	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2718091	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2718092	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2718097	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2718100	0.90[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	0.94[AFR][1000 genomes]
rs4731567	1.00[EUR][1000 genomes]
rs6467234	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6467236	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6949882	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6950279	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6950496	0.91[AFR][1000 genomes]
rs6970267	0.98[AFR][1000 genomes]
rs71529418	0.89[AFR][1000 genomes]
rs71577870	0.89[AFR][1000 genomes]
rs7805353	0.87[AMR][1000 genomes]
rs9641847	1.00[EUR][1000 genomes]
rs9641848	0.95[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:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128866000-128902200	Weak transcription	Gastric	stomach
2	chr7:128866200-128898600	Weak transcription	Thymus	Thymus
3	chr7:128866400-128891400	Weak transcription	Fetal Stomach	stomach
4	chr7:128866400-128899000	Weak transcription	Ovary	ovary
5	chr7:128866600-128901400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr7:128866800-128889600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr7:128867000-128898400	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr7:128867200-128909800	Weak transcription	Primary B cells from cord blood	blood
9	chr7:128867600-128885600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr7:128868600-128897200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr7:128872800-128892000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr7:128876400-128889800	Weak transcription	Fetal Intestine Small	intestine
13	chr7:128878800-128897000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr7:128880400-128889800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr7:128880600-128887000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr7:128881000-128892000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr7:128881000-128898800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:128882000-128899600	Weak transcription	Left Ventricle	heart
19	chr7:128882200-128888000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr7:128884400-128885600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:128884400-128887000	Weak transcription	NHEK	skin
22	chr7:128884400-128888000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr7:128884600-128887200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr7:128884800-128898800	Weak transcription	Primary T cells from cord blood	blood

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