Variant report

Variant	rs1257769
Chromosome Location	chr11:94153925-94153926
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	chr11:94151210..94154099-chr11:94225020..94227256,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168876	Chromatin interaction
ENSG00000020922	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10831225	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11020802	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11020803	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12224966	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1272743	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3017077	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474577	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs509723	0.88[AMR][1000 genomes]
rs509744	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs518640	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs521349	0.86[AMR][1000 genomes]
rs530569	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs535801	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs540199	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs550255	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56108804	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs563807	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs588701	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59678918	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs625245	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs639311	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs641936	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs654718	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs657249	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs680695	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs948575	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[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	nsv832233	chr11:93981434-94158471	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	esv1795745	chr11:94144987-94227993	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv1798271	chr11:94144987-94227993	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs1257769	RP11-685N10.1	cis	Stomach	GTEx
rs1257769	RP11-685N10.1	cis	Artery Aorta	GTEx
rs1257769	MRE11A	cis	Stomach	GTEx
rs1257769	MRE11A	cis	Thyroid	GTEx
rs1257769	RP11-685N10.1	cis	Thyroid	GTEx
rs1257769	MRE11A	cis	Skin Sun Exposed Lower leg	GTEx
rs1257769	RP11-685N10.1	cis	Muscle Skeletal	GTEx
rs1257769	RP11-685N10.1	cis	Esophagus Mucosa	GTEx
rs1257769	MRE11A	cis	lung	GTEx
rs1257769	RP11-685N10.1	cis	Heart Left Ventricle	GTEx
rs1257769	RP11-685N10.1	cis	lung	GTEx
rs1257769	MRE11A	cis	Heart Left Ventricle	GTEx
rs1257769	MRE11A	cis	Esophagus Muscularis	GTEx
rs1257769	RP11-685N10.1	cis	Artery Tibial	GTEx
rs1257769	RP11-685N10.1	cis	Esophagus Muscularis	GTEx
rs1257769	MRE11A	Cis_1M	lymphoblastoid	RTeQTL
rs1257769	RP11-685N10.1	cis	Nerve Tibial	GTEx
rs1257769	MRE11A	cis	Artery Aorta	GTEx
rs1257769	MRE11A	cis	Nerve Tibial	GTEx
rs1257769	MRE11A	cis	Whole Blood	GTEx
rs1257769	MRE11A	cis	Esophagus Mucosa	GTEx
rs1257769	MRE11A	cis	Adipose Subcutaneous	GTEx
rs1257769	RP11-685N10.1	cis	Adipose Subcutaneous	GTEx
rs1257769	MRE11A	cis	Artery Tibial	GTEx
rs1257769	RP11-685N10.1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:94135200-94161400	Weak transcription	Placenta	Placenta
2	chr11:94135200-94162200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr11:94138600-94162200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr11:94141200-94155000	Weak transcription	Primary T cells from cord blood	blood
5	chr11:94141800-94156600	Weak transcription	Spleen	Spleen
6	chr11:94142000-94154800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr11:94142400-94161200	Weak transcription	Brain Anterior Caudate	brain
8	chr11:94142600-94154800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr11:94142800-94156000	Weak transcription	Thymus	Thymus
10	chr11:94143200-94156400	Weak transcription	Fetal Stomach	stomach
11	chr11:94143400-94156400	Weak transcription	Gastric	stomach
12	chr11:94143600-94154800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr11:94143600-94156400	Weak transcription	Lung	lung
14	chr11:94143800-94156200	Weak transcription	Fetal Intestine Small	intestine
15	chr11:94143800-94156400	Weak transcription	Ovary	ovary
16	chr11:94144200-94169200	Weak transcription	Aorta	Aorta
17	chr11:94145000-94156400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:94145000-94161800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr11:94145400-94154800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr11:94145400-94162000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr11:94146200-94156400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr11:94146400-94161200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr11:94146600-94154800	Weak transcription	Fetal Thymus	thymus
24	chr11:94146800-94156400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr11:94146800-94156800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr11:94146800-94156800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr11:94146800-94156800	Weak transcription	Fetal Lung	lung
28	chr11:94146800-94157000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr11:94146800-94160800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr11:94146800-94161400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr11:94147000-94154400	Weak transcription	GM12878-XiMat	blood
32	chr11:94147000-94155000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr11:94147000-94156600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr11:94147200-94154800	Weak transcription	Left Ventricle	heart
35	chr11:94147200-94156400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr11:94147200-94156600	Weak transcription	Right Ventricle	heart
37	chr11:94147200-94162200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr11:94147400-94161000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr11:94147600-94154600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr11:94147600-94154800	Weak transcription	Fetal Muscle Leg	muscle
41	chr11:94147600-94161000	Weak transcription	Brain Hippocampus Middle	brain
42	chr11:94147600-94162000	Weak transcription	HepG2	liver
43	chr11:94147800-94161400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr11:94148000-94154600	Weak transcription	Hela-S3	cervix
45	chr11:94148800-94156000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr11:94149000-94154800	Weak transcription	Adipose Nuclei	Adipose
47	chr11:94149000-94156200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr11:94149000-94156800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr11:94149000-94166600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr11:94149200-94154400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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