Variant report

Variant	rs2402890
Chromosome Location	chr7:127977352-127977353
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	chr7:127973213..127977895-chr7:127980902..127985287,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238750	Chromatin interaction
ENSG00000106344	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11069	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17151983	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17151987	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17151996	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17152000	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17152002	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs41281728	1.00[EUR][1000 genomes]
rs41281731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55667068	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55913412	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56007906	1.00[EUR][1000 genomes]
rs6467170	0.98[EUR][1000 genomes]
rs6467174	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6952533	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6980001	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6980301	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs723627	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73228315	0.83[EUR][1000 genomes]
rs73230631	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73230632	1.00[EUR][1000 genomes]
rs73230633	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73230642	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73230649	1.00[EUR][1000 genomes]
rs73230652	1.00[EUR][1000 genomes]
rs73230654	1.00[EUR][1000 genomes]
rs73230656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73230657	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73230659	1.00[EUR][1000 genomes]
rs73721355	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73721362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7800186	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7804796	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831124	chr7:127970345-128147910	Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv889191	chr7:127973133-128073326	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127939600-127982200	Weak transcription	Stomach Mucosa	stomach
2	chr7:127940000-127980800	Strong transcription	Fetal Muscle Trunk	muscle
3	chr7:127940400-127980000	Strong transcription	Stomach Smooth Muscle	stomach
4	chr7:127940600-127980000	Strong transcription	Liver	Liver
5	chr7:127941600-127979600	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:127941600-127980000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr7:127942000-127980400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:127942000-127980600	Strong transcription	Fetal Muscle Leg	muscle
9	chr7:127942600-127979600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr7:127943000-127979800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:127943000-127979800	Strong transcription	Fetal Intestine Large	intestine
12	chr7:127943000-127981200	Strong transcription	Dnd41	blood
13	chr7:127943000-127982000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr7:127943200-127980400	Strong transcription	Duodenum Mucosa	Duodenum
15	chr7:127943200-127981600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr7:127943400-127979400	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr7:127943400-127979800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr7:127943400-127980000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr7:127943400-127980000	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr7:127943400-127980000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr7:127943400-127981400	Strong transcription	Primary B cells from peripheral blood	blood
22	chr7:127943400-127981600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr7:127944400-127980000	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr7:127944400-127980000	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr7:127944400-127980200	Strong transcription	Placenta	Placenta
26	chr7:127944400-127980600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr7:127945200-127980000	Strong transcription	GM12878-XiMat	blood
28	chr7:127945400-127979200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr7:127945600-127979400	Strong transcription	Brain Germinal Matrix	brain
30	chr7:127949600-127978800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr7:127949600-127980000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr7:127952000-127979800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr7:127953800-127982600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr7:127955600-127980000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr7:127955800-127982800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr7:127956400-127978600	Strong transcription	Fetal Stomach	stomach
37	chr7:127956800-127977400	Strong transcription	Ovary	ovary
38	chr7:127958000-127980600	Strong transcription	K562	blood
39	chr7:127961400-127979800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr7:127961400-127980000	Strong transcription	Fetal Thymus	thymus
41	chr7:127961600-127980000	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr7:127962200-127980600	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr7:127962400-127980200	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr7:127963000-127979800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr7:127963000-127980000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr7:127963000-127980400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr7:127963200-127980000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr7:127963400-127981200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr7:127963800-127979800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr7:127963800-127980600	Strong transcription	Skeletal Muscle Female	skeletal muscle

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