Variant report

Variant	rs2513003
Chromosome Location	chr11:86448385-86448386
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:86430742..86432818-chr11:86447067..86449171,2	MCF-7	breast:
2	chr11:86446644..86449202-chr11:86509894..86512786,2	MCF-7	breast:
3	chr11:86390068..86392498-chr11:86447333..86449140,2	MCF-7	breast:
4	chr11:86445788..86450763-chr11:86452280..86455324,5	K562	blood:
5	chr11:86445700..86450143-chr11:86450733..86453676,4	MCF-7	breast:
6	chr11:86446536..86448977-chr8:126441223..126442943,2	MCF-7	breast:
7	chr11:86445661..86448422-chr11:86500757..86504196,4	MCF-7	breast:
8	chr11:86442349..86444552-chr11:86447054..86448697,2	MCF-7	breast:
9	chr11:86415734..86419675-chr11:86447085..86451465,5	MCF-7	breast:
10	chr11:86447300..86456471-chr11:86483287..86490697,27	MCF-7	breast:
11	chr11:86446334..86448722-chr11:86490852..86493629,3	MCF-7	breast:
12	chr11:86445705..86457398-chr11:86504607..86518485,46	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000150687	Chromatin interaction
ENSG00000173334	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1075702	0.91[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs11234783	0.82[ASN][1000 genomes]
rs12420039	0.80[MEX][hapmap]
rs17211787	0.86[MEX][hapmap]
rs17211926	0.81[CHB][hapmap]
rs17819068	0.81[CHB][hapmap]
rs17819187	0.80[MEX][hapmap]
rs1939111	0.80[MEX][hapmap]
rs2433406	0.90[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2433407	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2433408	0.90[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2433409	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2433410	0.88[ASN][1000 genomes]
rs2433411	0.93[ASN][1000 genomes]
rs2433424	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2433425	0.94[ASN][1000 genomes]
rs2433426	0.95[ASN][1000 genomes]
rs2433427	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2433428	0.97[ASN][1000 genomes]
rs2433429	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2433430	0.86[ASN][1000 genomes]
rs2433431	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2433432	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2433433	0.95[CHB][hapmap];0.89[CHD][hapmap];0.87[MEX][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2433434	0.95[CHB][hapmap];0.87[CHD][hapmap];0.87[MEX][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2433435	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs2433436	0.95[CHB][hapmap];0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs2433438	0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[ASN][1000 genomes]
rs2433439	0.95[CHB][hapmap];0.84[CHD][hapmap];0.93[MEX][hapmap];0.83[ASN][1000 genomes]
rs2433440	0.82[ASN][1000 genomes]
rs2433441	0.82[ASN][1000 genomes]
rs2512978	0.82[ASN][1000 genomes]
rs2512979	0.82[ASN][1000 genomes]
rs2512996	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2512997	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2512998	0.92[ASN][1000 genomes]
rs2512999	0.98[ASN][1000 genomes]
rs2513000	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2513001	0.96[ASN][1000 genomes]
rs2513004	0.88[EUR][1000 genomes]
rs2513005	0.91[CHB][hapmap]
rs2513006	0.94[ASN][1000 genomes]
rs2513008	0.90[ASN][1000 genomes]
rs2513009	0.91[ASN][1000 genomes]
rs2513010	0.92[ASN][1000 genomes]
rs2513011	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2513012	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2513018	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs2513019	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3096711	0.90[ASN][1000 genomes]
rs3096714	0.92[ASN][1000 genomes]
rs3096715	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs3096716	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs3809048	0.86[MEX][hapmap]
rs4128368	0.81[CHB][hapmap];0.80[MEX][hapmap]
rs4245426	0.84[ASN][1000 genomes]
rs4269941	0.81[CHB][hapmap];0.80[MEX][hapmap]
rs4304806	0.80[MEX][hapmap]
rs4586194	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4943957	0.82[ASN][1000 genomes]
rs7108176	0.93[ASN][1000 genomes]
rs7108300	0.92[ASN][1000 genomes]
rs7124794	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7129902	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1055071	chr11:86301240-86465465	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv428263	chr11:86357990-86508480	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1049157	chr11:86409059-86504155	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv521505	chr11:86438115-86515072	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2513003	TMEM126B	cis	parietal	SCAN
rs2513003	PRCP	cis	cerebellum	SCAN
rs2513003	CCDC83	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86407000-86451600	Weak transcription	Left Ventricle	heart
2	chr11:86424200-86449800	Weak transcription	Pancreas	Pancrea
3	chr11:86446000-86451600	Enhancers	NHLF	lung
4	chr11:86446000-86451800	Enhancers	HUVEC	blood vessel
5	chr11:86446000-86452000	Enhancers	HSMM	muscle
6	chr11:86446000-86458000	Enhancers	HMEC	breast
7	chr11:86446200-86448600	Enhancers	Fetal Brain Male	brain
8	chr11:86446200-86452000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr11:86446200-86452000	Enhancers	NH-A	brain
10	chr11:86446200-86452000	Enhancers	Osteobl	bone
11	chr11:86446200-86453200	Enhancers	Fetal Lung	lung
12	chr11:86446400-86448400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:86446400-86449000	Enhancers	HSMMtube	muscle
14	chr11:86446400-86455200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr11:86446600-86452600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:86446600-86453400	Enhancers	Fetal Stomach	stomach
17	chr11:86446800-86450800	Weak transcription	Esophagus	oesophagus
18	chr11:86446800-86455400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr11:86447000-86450000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:86447200-86448400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr11:86447200-86448400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:86447200-86449000	Weak transcription	NHEK	skin
23	chr11:86447200-86450800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:86447200-86451000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr11:86447400-86448400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr11:86447400-86448400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:86447400-86449000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr11:86447400-86450200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr11:86447400-86451000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr11:86447400-86455200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr11:86447600-86451000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr11:86447600-86451600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr11:86447600-86454200	Enhancers	NHDF-Ad	bronchial
34	chr11:86447800-86448800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr11:86447800-86448800	Enhancers	Lung	lung
36	chr11:86447800-86449200	Enhancers	Psoas Muscle	Psoas
37	chr11:86447800-86449200	Enhancers	Stomach Smooth Muscle	stomach
38	chr11:86447800-86453400	Enhancers	Fetal Muscle Leg	muscle
39	chr11:86447800-86453800	Enhancers	Ovary	ovary
40	chr11:86448000-86448600	Enhancers	Fetal Thymus	thymus
41	chr11:86448000-86449200	Enhancers	Right Atrium	heart
42	chr11:86448000-86449400	Enhancers	Colon Smooth Muscle	Colon
43	chr11:86448000-86449600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr11:86448000-86449800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr11:86448000-86449800	Enhancers	A549	lung
46	chr11:86448000-86449800	Enhancers	Hela-S3	cervix
47	chr11:86448000-86450000	Enhancers	Rectal Smooth Muscle	rectum
48	chr11:86448000-86451000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr11:86448000-86452000	Enhancers	Muscle Satellite Cultured Cells	--
50	chr11:86448200-86450800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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