Variant report

Variant	rs17133461
Chromosome Location	chr11:74499824-74499825
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74494044..74497325-chr11:74499234..74501593,3	K562	blood:
2	chr11:74459598..74461734-chr11:74498287..74500805,2	MCF-7	breast:
3	chr11:74491588..74493349-chr11:74499824..74502526,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166439	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 28 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10160410	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10751241	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10793105	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10793107	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10793108	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10899042	0.88[CHD][hapmap]
rs10899045	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10899051	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10899052	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11236236	0.84[CHD][hapmap]
rs11236244	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12221841	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12223417	0.95[JPT][hapmap]
rs12225372	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12225387	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12417156	0.84[CHD][hapmap]
rs12419113	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12419929	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12421899	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12574850	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12575200	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12576129	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]
rs12576444	0.84[CHD][hapmap]
rs12577614	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1433771	0.81[CHD][hapmap]
rs2119028	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2165162	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2165163	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2298746	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2304683	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3814726	0.84[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4483614	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4944061	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]
rs4944944	0.84[CHD][hapmap]
rs4944947	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs4944950	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][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]
rs4944960	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4944961	0.84[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4944963	0.83[AMR][1000 genomes]
rs59143825	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59328242	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61671395	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61734374	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61894779	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61894839	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7102619	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7103136	0.88[CHD][hapmap];0.91[JPT][hapmap]
rs7105085	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7128739	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs725460	0.81[AMR][1000 genomes]
rs7396866	0.92[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap]
rs7928381	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs919877	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs968305	0.83[CHD][hapmap]
rs9787775	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9787897	0.89[AMR][1000 genomes];0.88[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:28)

SNP	Gene	Cis/trans	Tissue	Source
rs17133461	RP11-147I3.1	cis	Muscle Skeletal	GTEx
rs17133461	KCTD21	cis	cerebellum	SCAN
rs17133461	XRRA1	cis	Whole Blood	GTEx
rs17133461	RNF169	cis	cerebellum	SCAN
rs17133461	XRRA1	cis	lymphoblastoid	seeQTL
rs17133461	RNF169	cis	lymphoblastoid	seeQTL
rs17133461	XRRA1	cis	Thyroid	GTEx
rs17133461	XRRA1	cis	lesional skin	skin_eQTL
rs17133461	RP11-147I3.1	cis	Esophagus Muscularis	GTEx
rs17133461	XRRA1	cis	Adipose Subcutaneous	GTEx
rs17133461	XRRA1	cis	Nerve Tibial	GTEx
rs17133461	XRRA1	cis	lymphoblastoid	GTEx
rs17133461	PLEKHB1	cis	cerebellum	SCAN
rs17133461	XRRA1	cis	Artery Tibial	GTEx
rs17133461	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs17133461	PAAF1	cis	parietal	SCAN
rs17133461	XRRA1	cis	Muscle Skeletal	GTEx
rs17133461	XRRA1	cis	Stomach	GTEx
rs17133461	RP11-147I3.1	cis	Thyroid	GTEx
rs17133461	XRRA1	cis	parietal	SCAN
rs17133461	XRRA1	cis	cerebellum	SCAN
rs17133461	XRRA1	cis	normal skin	skin_eQTL
rs17133461	XRRA1	cis	Heart Left Ventricle	GTEx
rs17133461	XRRA1	cis	lung	GTEx
rs17133461	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs17133461	XRRA1	cis	Esophagus Muscularis	GTEx
rs17133461	XRRA1	cis	Artery Aorta	GTEx
rs17133461	XRRA1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74468000-74500800	Weak transcription	HepG2	liver
2	chr11:74470600-74500800	Weak transcription	Fetal Muscle Leg	muscle
3	chr11:74478000-74501600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:74480200-74501400	Weak transcription	Fetal Intestine Small	intestine
5	chr11:74485200-74502600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:74488400-74503800	Weak transcription	Stomach Mucosa	stomach
7	chr11:74488800-74500000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr11:74489800-74500800	Weak transcription	Left Ventricle	heart
9	chr11:74491600-74501000	Weak transcription	Fetal Brain Female	brain
10	chr11:74492000-74501800	Weak transcription	K562	blood
11	chr11:74492200-74500600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr11:74492200-74502400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:74492400-74500200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:74492400-74500800	Weak transcription	Placenta	Placenta
15	chr11:74492400-74501000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr11:74492400-74501200	Weak transcription	Fetal Lung	lung
17	chr11:74493600-74501400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:74493600-74501600	Weak transcription	Aorta	Aorta
19	chr11:74494600-74500000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr11:74494600-74501400	Weak transcription	HSMMtube	muscle
21	chr11:74494800-74500600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr11:74494800-74500800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:74494800-74500800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr11:74494800-74500800	Weak transcription	Brain Germinal Matrix	brain
25	chr11:74494800-74500800	Weak transcription	Fetal Stomach	stomach
26	chr11:74494800-74501400	Weak transcription	Brain Anterior Caudate	brain
27	chr11:74494800-74501400	Weak transcription	Thymus	Thymus
28	chr11:74494800-74530600	Weak transcription	NH-A	brain
29	chr11:74495000-74500600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr11:74495000-74500800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr11:74495000-74500800	Weak transcription	Brain Substantia Nigra	brain
32	chr11:74495000-74500800	Weak transcription	A549	lung
33	chr11:74495000-74501000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr11:74495200-74500800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr11:74495600-74500600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr11:74495600-74500800	Weak transcription	Hela-S3	cervix
37	chr11:74495600-74500800	Weak transcription	NHEK	skin
38	chr11:74495600-74501000	Weak transcription	HMEC	breast
39	chr11:74495600-74501600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr11:74495800-74500800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr11:74495800-74500800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr11:74495800-74500800	Weak transcription	Brain Hippocampus Middle	brain
43	chr11:74495800-74500800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr11:74495800-74500800	Weak transcription	Duodenum Mucosa	Duodenum
45	chr11:74495800-74500800	Weak transcription	Esophagus	oesophagus
46	chr11:74495800-74500800	Weak transcription	NHLF	lung
47	chr11:74495800-74501000	Weak transcription	Primary hematopoietic stem cells	blood
48	chr11:74495800-74501000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr11:74495800-74501000	Weak transcription	Fetal Kidney	kidney
50	chr11:74495800-74501000	Weak transcription	Fetal Thymus	thymus

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