Variant report

Variant	rs7128739
Chromosome Location	chr11:74573010-74573011
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74459057..74461401-chr11:74571503..74573260,2	MCF-7	breast:
2	chr11:74565498..74567149-chr11:74571743..74574550,2	K562	blood:
3	chr11:74556453..74558294-chr11:74572281..74574245,2	K562	blood:
4	chr11:74565498..74567871-chr11:74571743..74574141,2	K562	blood:

Variant related genes	Relation type
ENSG00000242999	Chromatin interaction
ENSG00000166439	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 27 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10160410	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10751241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10793105	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10793107	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10793108	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10899042	0.81[CHD][hapmap]
rs10899045	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10899051	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10899052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10899053	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs10899058	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs11236244	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11236281	0.87[CEU][hapmap];0.94[JPT][hapmap]
rs11236282	0.91[CEU][hapmap];0.95[JPT][hapmap]
rs11236294	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs11603294	0.89[CEU][hapmap];0.95[JPT][hapmap]
rs12221841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12223417	0.95[JPT][hapmap]
rs12225372	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12225387	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12419113	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12419929	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12421899	0.93[EUR][1000 genomes]
rs12574850	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12575200	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12576129	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12577127	0.92[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs12577614	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1371410	0.92[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs17133461	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]
rs2119028	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2165162	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2165163	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2298746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304683	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3814726	0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4245440	0.92[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs4387374	0.92[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs4483614	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];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4944061	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4944947	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs4944950	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4944960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944961	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59143825	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59328242	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61671395	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61734374	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61894779	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61894839	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7102619	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7103136	0.81[CHD][hapmap];0.91[JPT][hapmap]
rs7105085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7396866	0.92[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs7483351	0.90[CEU][hapmap];0.95[JPT][hapmap]
rs7928381	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs919877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9787775	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9787897	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv832210	chr11:74562782-74732133	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:27)

SNP	Gene	Cis/trans	Tissue	Source
rs7128739	RP11-147I3.1	cis	Thyroid	GTEx
rs7128739	XRRA1	cis	Muscle Skeletal	GTEx
rs7128739	XRRA1	cis	Thyroid	GTEx
rs7128739	RNF169	cis	multi-tissue	Pritchard
rs7128739	RP11-147I3.1	cis	Muscle Skeletal	GTEx
rs7128739	XRRA1	cis	parietal	SCAN
rs7128739	XRRA1	cis	Heart Left Ventricle	GTEx
rs7128739	RNF169	cis	cerebellum	SCAN
rs7128739	PLEKHB1	cis	cerebellum	SCAN
rs7128739	XRRA1	cis	multi-tissue	Pritchard
rs7128739	XRRA1	cis	Whole Blood	GTEx
rs7128739	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs7128739	RNF169	cis	lymphoblastoid	seeQTL
rs7128739	PAAF1	cis	parietal	SCAN
rs7128739	XRRA1	cis	Adipose Subcutaneous	GTEx
rs7128739	XRRA1	cis	cerebellum	SCAN
rs7128739	XRRA1	cis	Artery Aorta	GTEx
rs7128739	XRRA1	cis	lung	GTEx
rs7128739	XRRA1	cis	Stomach	GTEx
rs7128739	XRRA1	cis	Esophagus Mucosa	GTEx
rs7128739	XRRA1	cis	lymphoblastoid	GTEx
rs7128739	XRRA1	cis	Esophagus Muscularis	GTEx
rs7128739	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs7128739	XRRA1	cis	lymphoblastoid	seeQTL
rs7128739	KCTD21	cis	cerebellum	SCAN
rs7128739	XRRA1	cis	Nerve Tibial	GTEx
rs7128739	XRRA1	cis	Artery Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74528000-74576400	Weak transcription	Stomach Mucosa	stomach
2	chr11:74552800-74576800	Strong transcription	Stomach Smooth Muscle	stomach
3	chr11:74562200-74595800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:74563200-74573600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr11:74563400-74576600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr11:74563600-74576400	Weak transcription	Colon Smooth Muscle	Colon
7	chr11:74564800-74576600	Weak transcription	NH-A	brain
8	chr11:74567200-74575600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr11:74567200-74576200	Strong transcription	Primary T cells from cord blood	blood
10	chr11:74567400-74576000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr11:74567600-74575200	Strong transcription	Brain Inferior Temporal Lobe	brain
12	chr11:74567600-74576400	Strong transcription	Brain Anterior Caudate	brain
13	chr11:74569200-74574600	Strong transcription	Osteobl	bone
14	chr11:74569400-74575600	Strong transcription	Brain Hippocampus Middle	brain
15	chr11:74569600-74574600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr11:74569600-74574800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr11:74569600-74575000	Strong transcription	Fetal Kidney	kidney
18	chr11:74569600-74576000	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr11:74569800-74575200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
20	chr11:74569800-74575200	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr11:74569800-74576000	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr11:74569800-74576200	Strong transcription	Placenta Amnion	Placenta Amnion
23	chr11:74569800-74577200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr11:74569800-74588400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr11:74570000-74575200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
26	chr11:74570000-74576400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr11:74570000-74577000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
28	chr11:74570000-74588400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr11:74570200-74573200	Weak transcription	K562	blood
30	chr11:74570200-74573600	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
31	chr11:74570200-74575600	Strong transcription	Pancreas	Pancrea
32	chr11:74570600-74573400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
33	chr11:74570600-74578800	ZNF genes & repeats	Fetal Brain Female	brain
34	chr11:74570600-74585600	ZNF genes & repeats	Dnd41	blood
35	chr11:74570600-74588400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
36	chr11:74570800-74573400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr11:74570800-74573600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
38	chr11:74570800-74574000	ZNF genes & repeats	Lung	lung
39	chr11:74570800-74574400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr11:74570800-74574800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
41	chr11:74570800-74574800	ZNF genes & repeats	GM12878-XiMat	blood
42	chr11:74570800-74575200	Strong transcription	Gastric	stomach
43	chr11:74570800-74576800	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr11:74570800-74578800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:74570800-74579400	ZNF genes & repeats	Fetal Intestine Small	intestine
46	chr11:74570800-74579800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
47	chr11:74570800-74584800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr11:74571000-74573800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr11:74571000-74573800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
50	chr11:74571000-74588400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood

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