Variant report

Variant	rs1888004
Chromosome Location	chr13:111019895-111019896
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	chr13:110998747..111001363-chr13:111017534..111020102,2	MCF-7	breast:
2	chr13:111016706..111018385-chr13:111018819..111020649,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11838637	0.81[ASN][1000 genomes]
rs1888005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4773169	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4773170	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4773171	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4773173	0.81[ASN][1000 genomes]
rs7318424	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7333596	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7333748	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7334022	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs750598	0.81[ASN][1000 genomes]
rs7999034	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs872587	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs872588	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs872589	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs913746	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9515195	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9515196	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9515197	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9521717	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9521718	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9521719	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9521720	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9521721	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs952359	0.81[ASN][1000 genomes]
rs9555692	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9555694	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9559780	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9559781	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv1038914	chr13:110860219-111190104	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111002400-111026000	Weak transcription	Psoas Muscle	Psoas
2	chr13:111007400-111023000	Weak transcription	A549	lung
3	chr13:111007600-111020400	Weak transcription	Fetal Kidney	kidney
4	chr13:111007600-111030600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr13:111007600-111031000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr13:111007600-111031400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr13:111008400-111020000	Weak transcription	HMEC	breast
8	chr13:111009000-111024000	Weak transcription	Pancreas	Pancrea
9	chr13:111009000-111029400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr13:111010400-111024000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:111011000-111022000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr13:111011000-111024000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr13:111011000-111032000	Weak transcription	Gastric	stomach
14	chr13:111011000-111032400	Weak transcription	NHEK	skin
15	chr13:111011200-111029800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr13:111013800-111023400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr13:111014200-111024000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr13:111014200-111027400	Weak transcription	Spleen	Spleen
19	chr13:111014400-111020000	Weak transcription	Fetal Lung	lung
20	chr13:111014400-111025800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr13:111014400-111029000	Weak transcription	HSMM	muscle
22	chr13:111014600-111024000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr13:111014800-111029600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr13:111015400-111020000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr13:111015400-111023400	Weak transcription	NHDF-Ad	bronchial
26	chr13:111015600-111023000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr13:111015600-111036600	Weak transcription	Fetal Intestine Small	intestine
28	chr13:111015800-111022600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr13:111016200-111020600	Enhancers	Fetal Heart	heart
30	chr13:111016200-111023400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr13:111016200-111024000	Weak transcription	Right Ventricle	heart
32	chr13:111016800-111024000	Weak transcription	Ovary	ovary
33	chr13:111017800-111020600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr13:111018000-111020600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr13:111018200-111020200	Weak transcription	Fetal Stomach	stomach
36	chr13:111018200-111022000	Weak transcription	Lung	lung
37	chr13:111018200-111023000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr13:111018200-111024000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr13:111018200-111024000	Weak transcription	Right Atrium	heart
40	chr13:111018400-111021200	Strong transcription	Osteobl	bone
41	chr13:111018400-111023600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr13:111018400-111024000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr13:111018400-111025800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr13:111018600-111023200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr13:111018800-111020000	Strong transcription	HUVEC	blood vessel
46	chr13:111019200-111020600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr13:111019400-111020200	Genic enhancers	Fetal Muscle Leg	muscle
48	chr13:111019400-111020400	Enhancers	Placenta	Placenta
49	chr13:111019400-111023000	Weak transcription	HSMMtube	muscle
50	chr13:111019400-111023200	Weak transcription	Adipose Nuclei	Adipose

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