Variant report

Variant	rs4944950
Chromosome Location	chr11:74481631-74481632
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74457889..74463104-chr11:74478763..74484936,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166439	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 44 )

rSNPs within LD-proxies of this variant (count:57)

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]
rs10899042	0.88[CHD][hapmap]
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]
rs11236236	0.84[CHD][hapmap]
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]
rs12417156	0.84[CHD][hapmap]
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]
rs12576129	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]
rs12576444	0.84[CHD][hapmap]
rs12577614	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1433771	0.81[CHD][hapmap]
rs17133461	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]
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];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][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];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[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];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3814726	0.84[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.82[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];0.96[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][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]
rs4944944	0.84[CHD][hapmap]
rs4944947	0.88[CHD][hapmap];0.82[JPT][hapmap];0.81[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	0.84[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];0.91[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][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	0.88[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];0.96[MEX][hapmap];1.00[TSI][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];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]
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]
rs968305	0.83[CHD][hapmap]
rs9787775	0.96[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:9 , 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	esv1840811	chr11:74452658-74488369	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	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
9	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:44)

SNP	Gene	Cis/trans	Tissue	Source
rs4944950	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs4944950	RP11-147I3.1	cis	Esophagus Muscularis	GTEx
rs4944950	XRRA1	cis	cerebellum	SCAN
rs4944950	RNF169	cis	multi-tissue	Pritchard
rs4944950	XRRA1	trans	brain	seeQTL
rs4944950	RP11-147I3.1	cis	Thyroid	GTEx
rs4944950	XRRA1,RNF169	cis	thalamus	BrainEAC
rs4944950	XRRA1	cis	Thyroid	GTEx
rs4944950	XRRA1	cis	Esophagus Muscularis	GTEx
rs4944950	KCTD21	cis	cerebellum	SCAN
rs4944950	XRRA1	cis	Artery Tibial	GTEx
rs4944950	XRRA1,RNF169	cis	frontal cortex	BrainEAC
rs4944950	PLEKHB1	cis	cerebellum	SCAN
rs4944950	XRRA1,RNF169	cis	substantia nigra	BrainEAC
rs4944950	XRRA1	cis	lesional skin	skin_eQTL
rs4944950	XRRA1,RNF169	cis	occipital cortex	BrainEAC
rs4944950	XRRA1	cis	Whole Blood	GTEx
rs4944950	XRRA1,RNF169	cis	cerebellar cortex	BrainEAC
rs4944950	RNF169	cis	cerebellum	SCAN
rs4944950	XRRA1	cis	Heart Left Ventricle	GTEx
rs4944950	XRRA1,RNF169	cis	inferior olivary nucleus	BrainEAC
rs4944950	XRRA1	cis	lymphoblastoid	seeQTL
rs4944950	XRRA1,RNF169	cis	intralobular white matter	BrainEAC
rs4944950	XRRA1	cis	normal skin	skin_eQTL
rs4944950	XRRA1	cis	lung	GTEx
rs4944950	XRRA1	cis	multi-tissue	Pritchard
rs4944950	RP11-147I3.1	cis	Muscle Skeletal	GTEx
rs4944950	XRRA1,RNF169	cis	hippocampus	BrainEAC
rs4944950	RNF169	cis	lymphoblastoid	seeQTL
rs4944950	XRRA1	cis	lymphoblastoid	GTEx
rs4944950	XRRA1	cis	brain	seeQTL
rs4944950	XRRA1,RNF169	cis	temporal cortex	BrainEAC
rs4944950	XRRA1,RNF169	cis	putamen	BrainEAC
rs4944950	XRRA1	cis	parietal	SCAN
rs4944950	XRRA1	cis	Artery Aorta	GTEx
rs4944950	XRRA1	cis	Muscle Skeletal	GTEx
rs4944950	XRRA1	cis	Stomach	GTEx
rs4944950	XRRA1	cis	Nerve Tibial	GTEx
rs4944950	XRRA1,RNF169	cis	brain	BrainEAC
rs4944950	XRRA1	cis	Liver	GTEx
rs4944950	PAAF1	cis	parietal	SCAN
rs4944950	CHRDL2	cis	multi-tissue	Pritchard
rs4944950	XRRA1	cis	Adipose Subcutaneous	GTEx
rs4944950	XRRA1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:58 , 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	chr11:74462600-74487800	Weak transcription	K562	blood
3	chr11:74467000-74494200	Weak transcription	Hela-S3	cervix
4	chr11:74467200-74483200	Weak transcription	Fetal Heart	heart
5	chr11:74467200-74490800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr11:74467200-74493200	Weak transcription	Pancreas	Pancrea
7	chr11:74467400-74486000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr11:74467800-74489000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:74468000-74484200	Weak transcription	NHDF-Ad	bronchial
10	chr11:74468000-74494000	Weak transcription	Dnd41	blood
11	chr11:74468000-74500800	Weak transcription	HepG2	liver
12	chr11:74470400-74494000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr11:74470600-74500800	Weak transcription	Fetal Muscle Leg	muscle
14	chr11:74474400-74484200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr11:74475200-74491200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr11:74475400-74494600	Weak transcription	Esophagus	oesophagus
17	chr11:74475600-74489000	Weak transcription	Left Ventricle	heart
18	chr11:74476200-74483200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr11:74476200-74493400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr11:74476200-74494400	Weak transcription	Fetal Stomach	stomach
21	chr11:74476600-74493200	Weak transcription	Right Atrium	heart
22	chr11:74477400-74487800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr11:74477800-74484200	Weak transcription	Osteobl	bone
24	chr11:74478000-74482200	Enhancers	Primary B cells from peripheral blood	blood
25	chr11:74478000-74501600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr11:74478800-74482400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr11:74479000-74482200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr11:74479000-74489000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr11:74479400-74484200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr11:74479600-74484400	Weak transcription	NHLF	lung
31	chr11:74479800-74488400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr11:74480200-74501400	Weak transcription	Fetal Intestine Small	intestine
33	chr11:74480400-74481800	Enhancers	Colon Smooth Muscle	Colon
34	chr11:74480400-74481800	Enhancers	Duodenum Mucosa	Duodenum
35	chr11:74480600-74481800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr11:74480600-74482800	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr11:74480600-74483800	Weak transcription	A549	lung
38	chr11:74480800-74482200	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr11:74481000-74481800	Enhancers	Primary B cells from cord blood	blood
40	chr11:74481000-74482000	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr11:74481000-74482200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr11:74481200-74481800	Enhancers	Primary T cells from cord blood	blood
43	chr11:74481200-74481800	Enhancers	Muscle Satellite Cultured Cells	--
44	chr11:74481200-74481800	Enhancers	NHEK	skin
45	chr11:74481200-74482000	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr11:74481200-74488400	Weak transcription	Lung	lung
47	chr11:74481200-74490800	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr11:74481200-74492800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr11:74481400-74481800	Flanking Active TSS	GM12878-XiMat	blood
50	chr11:74481400-74482400	Enhancers	Primary neutrophils fromperipheralblood	blood

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