Variant report

Variant	rs1058650
Chromosome Location	chr13:30340585-30340586
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:30339629..30341793-chr13:30342795..30344909,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11147398	0.83[ASN][1000 genomes]
rs12872400	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1323931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1410110	0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1854176	0.87[ASN][1000 genomes]
rs1927193	0.86[ASN][1000 genomes]
rs2025604	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2182129	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2234416	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2388246	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2388247	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.82[ASN][1000 genomes]
rs2761938	0.91[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap]
rs278049	0.82[CHB][hapmap]
rs35541102	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4083610	0.83[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs4238128	0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs4265673	0.91[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs4297554	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4387451	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4769772	0.88[ASN][1000 genomes]
rs4769775	0.83[ASN][1000 genomes]
rs6490429	0.82[ASN][1000 genomes]
rs6490430	0.82[ASN][1000 genomes]
rs72623487	0.95[ASN][1000 genomes]
rs7320474	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7326253	0.81[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs7330356	0.82[CHB][hapmap]
rs7335148	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7342470	0.85[ASN][1000 genomes]
rs765404	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7981622	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7995666	0.91[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs9314972	0.86[ASN][1000 genomes]
rs9314973	0.86[ASN][1000 genomes]
rs9314974	0.86[ASN][1000 genomes]
rs9314975	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9314978	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9506226	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9506229	0.91[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs9506231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9506233	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9508550	0.87[ASN][1000 genomes]
rs9508553	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9508554	0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs9508557	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9508558	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9508559	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9508560	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9508561	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9508564	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9550494	0.89[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs9551739	0.88[ASN][1000 genomes]
rs9551741	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9551744	0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs9551751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9551753	0.94[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs9578136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9578139	0.91[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899961	chr13:30226924-30407273	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30326600-30343200	Weak transcription	Spleen	Spleen
2	chr13:30328400-30340600	Weak transcription	NHLF	lung
3	chr13:30328600-30341200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr13:30328800-30340800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr13:30328800-30347800	Weak transcription	Fetal Kidney	kidney
6	chr13:30328800-30351800	Weak transcription	NH-A	brain
7	chr13:30328800-30352600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr13:30329200-30340600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:30329200-30351200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr13:30330600-30355000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr13:30333000-30340600	Weak transcription	Fetal Thymus	thymus
12	chr13:30333000-30340600	Weak transcription	Thymus	Thymus
13	chr13:30333200-30340600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr13:30333200-30353800	Weak transcription	Gastric	stomach
15	chr13:30333200-30360200	Weak transcription	Pancreas	Pancrea
16	chr13:30333200-30368200	Weak transcription	Aorta	Aorta
17	chr13:30333400-30340600	Weak transcription	Placenta	Placenta
18	chr13:30333400-30345800	Weak transcription	HepG2	liver
19	chr13:30333400-30357000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr13:30333600-30340600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr13:30333600-30376200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr13:30334800-30340800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr13:30335200-30356800	Weak transcription	GM12878-XiMat	blood
24	chr13:30335400-30349800	Weak transcription	Fetal Stomach	stomach
25	chr13:30335600-30340600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr13:30335800-30340600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr13:30336000-30340600	Weak transcription	Left Ventricle	heart
28	chr13:30336000-30343000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr13:30336200-30340600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr13:30336200-30340600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr13:30336400-30340600	Weak transcription	Fetal Lung	lung
32	chr13:30336400-30357000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr13:30336600-30353800	Weak transcription	Psoas Muscle	Psoas
34	chr13:30336800-30340600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr13:30337000-30340600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr13:30337600-30363000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr13:30337800-30340600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr13:30337800-30342800	Weak transcription	Esophagus	oesophagus
39	chr13:30337800-30359800	Weak transcription	HMEC	breast
40	chr13:30338000-30340600	Weak transcription	HUVEC	blood vessel
41	chr13:30338000-30340800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr13:30338200-30340600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr13:30338200-30341400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr13:30338200-30341600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr13:30338200-30343600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr13:30338200-30344000	Weak transcription	Ovary	ovary
47	chr13:30338400-30340600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr13:30338400-30340600	Weak transcription	Brain Anterior Caudate	brain
49	chr13:30338400-30341000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr13:30338400-30341200	Weak transcription	Fetal Muscle Leg	muscle

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