Variant report

Variant	rs12576129
Chromosome Location	chr11:74489069-74489070
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74476476..74478616-chr11:74487269..74490042,2	MCF-7	breast:
2	chr11:74486775..74489120-chr11:74491208..74495917,4	MCF-7	breast:
3	chr11:74487704..74490461-chr11:74495466..74498381,2	MCF-7	breast:
4	chr11:74458829..74461726-chr11:74487898..74491812,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166439	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10160410	0.81[EUR][1000 genomes]
rs10751241	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10793105	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10793107	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10793108	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10899045	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10899051	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10899052	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11236244	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12221841	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12223076	0.84[ASN][1000 genomes]
rs12223417	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12225372	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12225387	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12419113	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12419197	0.84[ASN][1000 genomes]
rs12419929	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12421899	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12574850	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12575200	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12577614	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17133461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2119028	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2165162	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2165163	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2298746	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2304683	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3814726	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4483614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4944061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944947	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs4944950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944960	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4944961	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4944963	0.82[AMR][1000 genomes]
rs59143825	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59328242	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61671395	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61734374	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61894779	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61894839	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6592594	0.85[ASN][1000 genomes]
rs7102619	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7103136	0.91[JPT][hapmap]
rs7105085	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7128739	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7928381	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs919877	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9787775	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9787897	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv932190	chr11:74359867-74618935	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases
7	nsv897916	chr11:74465068-74574677	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv897917	chr11:74474266-74595507	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs12576129	RP11-147I3.1	cis	Esophagus Muscularis	GTEx
rs12576129	XRRA1	cis	Whole Blood	GTEx
rs12576129	XRRA1	cis	Stomach	GTEx
rs12576129	XRRA1	cis	normal skin	skin_eQTL
rs12576129	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs12576129	XRRA1	cis	lung	GTEx
rs12576129	XRRA1	cis	Muscle Skeletal	GTEx
rs12576129	RP11-147I3.1	cis	Thyroid	GTEx
rs12576129	XRRA1	cis	Adipose Subcutaneous	GTEx
rs12576129	XRRA1	cis	Thyroid	GTEx
rs12576129	XRRA1	cis	lesional skin	skin_eQTL
rs12576129	XRRA1	cis	Esophagus Mucosa	GTEx
rs12576129	XRRA1	cis	Nerve Tibial	GTEx
rs12576129	XRRA1	cis	Esophagus Muscularis	GTEx
rs12576129	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs12576129	XRRA1	cis	Artery Aorta	GTEx
rs12576129	RP11-147I3.1	cis	Muscle Skeletal	GTEx
rs12576129	XRRA1	cis	Heart Left Ventricle	GTEx
rs12576129	XRRA1	cis	Artery Tibial	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74461600-74494000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr11:74467000-74494200	Weak transcription	Hela-S3	cervix
3	chr11:74467200-74490800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr11:74467200-74493200	Weak transcription	Pancreas	Pancrea
5	chr11:74468000-74494000	Weak transcription	Dnd41	blood
6	chr11:74468000-74500800	Weak transcription	HepG2	liver
7	chr11:74470400-74494000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:74470600-74500800	Weak transcription	Fetal Muscle Leg	muscle
9	chr11:74475200-74491200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr11:74475400-74494600	Weak transcription	Esophagus	oesophagus
11	chr11:74476200-74493400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr11:74476200-74494400	Weak transcription	Fetal Stomach	stomach
13	chr11:74476600-74493200	Weak transcription	Right Atrium	heart
14	chr11:74478000-74501600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr11:74480200-74501400	Weak transcription	Fetal Intestine Small	intestine
16	chr11:74481200-74490800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr11:74481200-74492800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr11:74481400-74494600	Weak transcription	Small Intestine	intestine
19	chr11:74481600-74490800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr11:74481600-74493400	Weak transcription	HSMM	muscle
21	chr11:74481600-74493800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr11:74481800-74492800	Weak transcription	NHEK	skin
23	chr11:74481800-74493800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr11:74481800-74494000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr11:74482200-74490000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr11:74482200-74490800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr11:74482200-74492000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr11:74482200-74493200	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr11:74482400-74493200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr11:74482800-74492000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr11:74483800-74497600	Weak transcription	Fetal Heart	heart
32	chr11:74484200-74489800	Weak transcription	GM12878-XiMat	blood
33	chr11:74484400-74490800	Weak transcription	Ovary	ovary
34	chr11:74484600-74491000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr11:74484600-74491400	Weak transcription	Fetal Lung	lung
36	chr11:74484600-74492800	Weak transcription	HUVEC	blood vessel
37	chr11:74485200-74494000	Weak transcription	HMEC	breast
38	chr11:74485200-74502600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr11:74485400-74491000	Weak transcription	Psoas Muscle	Psoas
40	chr11:74486000-74491800	Weak transcription	Right Ventricle	heart
41	chr11:74486400-74494000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr11:74486600-74497800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr11:74487200-74495400	Weak transcription	Fetal Kidney	kidney
44	chr11:74487400-74491600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr11:74487400-74491800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr11:74487600-74493400	Weak transcription	Thymus	Thymus
47	chr11:74487800-74489800	Enhancers	Rectal Smooth Muscle	rectum
48	chr11:74487800-74492400	Enhancers	Colon Smooth Muscle	Colon
49	chr11:74488000-74489400	Enhancers	Gastric	stomach
50	chr11:74488000-74491200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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