Variant report

Variant	rs7105085
Chromosome Location	chr11:74569939-74569940
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74555054..74558541-chr11:74569885..74572836,3	MCF-7	breast:
2	chr11:74569518..74572784-chr11:74573799..74577155,3	K562	blood:
3	chr11:74564462..74566139-chr11:74568773..74570851,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF169-2	chr11:74569914-74569995	NONHSAT022959

Variant related genes	Relation type
ENSG00000242999	Chromatin interaction
ENSG00000166435	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 30 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10160410	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10751241	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]
rs10793105	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793107	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10793108	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10899042	0.81[CHD][hapmap]
rs10899045	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899051	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10899052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10899053	0.91[CEU][hapmap];0.95[JPT][hapmap]
rs10899058	0.91[CEU][hapmap];0.95[JPT][hapmap]
rs11236244	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11236281	0.86[CEU][hapmap];0.95[JPT][hapmap]
rs11236282	0.91[CEU][hapmap];0.95[JPT][hapmap]
rs11236294	0.91[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];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12223417	0.95[JPT][hapmap]
rs12225372	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12225387	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12419113	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12419929	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12421899	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12574850	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12575200	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12576129	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]
rs12577127	0.91[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs12577614	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1371410	0.91[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs17133461	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]
rs2119028	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2165162	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2165163	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2298746	0.88[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304683	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3814726	0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4245440	0.91[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs4387374	0.91[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs4483614	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4944061	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]
rs4944947	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs4944950	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4944960	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];0.96[ASN][1000 genomes]
rs4944961	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4944963	0.84[AMR][1000 genomes]
rs59143825	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59328242	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61671395	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61734374	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61894779	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61894839	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7102619	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7103136	0.81[CHD][hapmap];0.91[JPT][hapmap]
rs7128739	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	0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes]
rs7483351	0.90[CEU][hapmap];0.95[JPT][hapmap]
rs7928381	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs919877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9787775	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9787897	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[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:30)

SNP	Gene	Cis/trans	Tissue	Source
rs7105085	XRRA1	cis	normal skin	skin_eQTL
rs7105085	XRRA1	cis	parietal	SCAN
rs7105085	RP11-147I3.1	cis	Muscle Skeletal	GTEx
rs7105085	RNF169	cis	cerebellum	SCAN
rs7105085	XRRA1	cis	Artery Aorta	GTEx
rs7105085	XRRA1	cis	Nerve Tibial	GTEx
rs7105085	XRRA1	cis	lymphoblastoid	GTEx
rs7105085	XRRA1	cis	Thyroid	GTEx
rs7105085	XRRA1	cis	lesional skin	skin_eQTL
rs7105085	XRRA1	cis	Esophagus Muscularis	GTEx
rs7105085	XRRA1	cis	lung	GTEx
rs7105085	PAAF1	cis	parietal	SCAN
rs7105085	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs7105085	RNF169	cis	multi-tissue	Pritchard
rs7105085	XRRA1	cis	multi-tissue	Pritchard
rs7105085	XRRA1	cis	Adipose Subcutaneous	GTEx
rs7105085	XRRA1	cis	Esophagus Mucosa	GTEx
rs7105085	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs7105085	RP11-147I3.1	cis	lung	GTEx
rs7105085	XRRA1	cis	Muscle Skeletal	GTEx
rs7105085	XRRA1	cis	Whole Blood	GTEx
rs7105085	KCTD21	cis	cerebellum	SCAN
rs7105085	XRRA1	cis	Stomach	GTEx
rs7105085	XRRA1	cis	Artery Tibial	GTEx
rs7105085	XRRA1	cis	lymphoblastoid	seeQTL
rs7105085	RP11-147I3.1	cis	Thyroid	GTEx
rs7105085	XRRA1	cis	cerebellum	SCAN
rs7105085	PLEKHB1	cis	cerebellum	SCAN
rs7105085	XRRA1	cis	Heart Left Ventricle	GTEx
rs7105085	RP11-147I3.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:124 , 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	chr11:74544200-74570800	Strong transcription	Duodenum Mucosa	Duodenum
3	chr11:74547600-74571400	Weak transcription	Fetal Brain Male	brain
4	chr11:74552800-74576800	Strong transcription	Stomach Smooth Muscle	stomach
5	chr11:74554800-74571600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:74559000-74571400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr11:74559200-74571400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr11:74559200-74571800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr11:74559400-74570000	Weak transcription	Right Ventricle	heart
10	chr11:74560600-74571200	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr11:74561200-74571200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr11:74561600-74571200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr11:74561800-74571000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr11:74562000-74571600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr11:74562200-74570000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:74562200-74595800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr11:74562400-74570400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr11:74563000-74571400	Weak transcription	Fetal Thymus	thymus
19	chr11:74563200-74570200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr11:74563200-74571800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:74563200-74573600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr11:74563400-74570000	Weak transcription	K562	blood
23	chr11:74563400-74576600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr11:74563600-74576400	Weak transcription	Colon Smooth Muscle	Colon
25	chr11:74563800-74570000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr11:74564000-74570000	Weak transcription	Esophagus	oesophagus
27	chr11:74564000-74571200	Weak transcription	HepG2	liver
28	chr11:74564000-74571800	Weak transcription	HUVEC	blood vessel
29	chr11:74564400-74570800	Weak transcription	GM12878-XiMat	blood
30	chr11:74564600-74570000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr11:74564800-74570600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr11:74564800-74576600	Weak transcription	NH-A	brain
33	chr11:74565200-74571200	Weak transcription	HMEC	breast
34	chr11:74565400-74570800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr11:74566600-74570800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr11:74567200-74570600	Strong transcription	Dnd41	blood
37	chr11:74567200-74571000	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr11:74567200-74571600	Strong transcription	Placenta	Placenta
39	chr11:74567200-74571800	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr11:74567200-74575600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr11:74567200-74576200	Strong transcription	Primary T cells from cord blood	blood
42	chr11:74567400-74570000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr11:74567400-74570400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr11:74567400-74570600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr11:74567400-74571600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr11:74567400-74571600	Strong transcription	Adipose Nuclei	Adipose
47	chr11:74567400-74571600	Strong transcription	Liver	Liver
48	chr11:74567400-74576000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr11:74567600-74570000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:74567600-74571200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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