Variant report

Variant	rs2304683
Chromosome Location	chr11:74563077-74563078
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 32 )

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];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10793105	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10793107	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10793108	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10899045	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10899051	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10899052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10899053	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs10899058	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs11236244	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11236281	0.87[CEU][hapmap];0.95[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12223417	0.95[JPT][hapmap]
rs12225372	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12225387	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12419113	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12419929	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12421899	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12574850	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12575200	0.94[AFR][1000 genomes];0.98[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];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12577127	0.92[CEU][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs12577614	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1371410	0.92[CEU][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs17133461	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]
rs2119028	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2165162	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2165163	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2298746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3814726	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4245440	0.92[CEU][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs4387374	0.92[CEU][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs4483614	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4944061	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]
rs4944947	0.82[JPT][hapmap]
rs4944950	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]
rs4944960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944961	0.84[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944963	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs59143825	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59328242	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61671395	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61734374	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61894779	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61894839	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7102619	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7103136	0.91[JPT][hapmap]
rs7105085	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]
rs7128739	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]
rs725460	0.83[AMR][1000 genomes]
rs7396866	0.92[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes]
rs7483351	0.90[CEU][hapmap];0.95[JPT][hapmap]
rs7928381	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs919877	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];0.99[ASN][1000 genomes]
rs9787775	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9787897	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[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:32)

SNP	Gene	Cis/trans	Tissue	Source
rs2304683	XRRA1	cis	Muscle Skeletal	GTEx
rs2304683	XRRA1	cis	Heart Left Ventricle	GTEx
rs2304683	XRRA1	cis	Esophagus Muscularis	GTEx
rs2304683	RP11-147I3.1	cis	Esophagus Muscularis	GTEx
rs2304683	XRRA1	trans	brain	seeQTL
rs2304683	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs2304683	XRRA1	cis	multi-tissue	Pritchard
rs2304683	XRRA1	cis	Esophagus Mucosa	GTEx
rs2304683	RP11-147I3.1	cis	Muscle Skeletal	GTEx
rs2304683	XRRA1	cis	Nerve Tibial	GTEx
rs2304683	RNF169	cis	cerebellum	SCAN
rs2304683	KCTD21	cis	cerebellum	SCAN
rs2304683	XRRA1	cis	brain	seeQTL
rs2304683	PLEKHB1	cis	cerebellum	SCAN
rs2304683	XRRA1	cis	Thyroid	GTEx
rs2304683	XRRA1	cis	normal skin	skin_eQTL
rs2304683	XRRA1	cis	Stomach	GTEx
rs2304683	XRRA1	cis	Artery Tibial	GTEx
rs2304683	XRRA1	cis	lesional skin	skin_eQTL
rs2304683	XRRA1	cis	lymphoblastoid	seeQTL
rs2304683	RNF169	cis	multi-tissue	Pritchard
rs2304683	PAAF1	cis	parietal	SCAN
rs2304683	XRRA1	cis	Whole Blood	GTEx
rs2304683	XRRA1	cis	Artery Aorta	GTEx
rs2304683	RP11-147I3.1	cis	Thyroid	GTEx
rs2304683	XRRA1	cis	parietal	SCAN
rs2304683	XRRA1	cis	cerebellum	SCAN
rs2304683	XRRA1	cis	lymphoblastoid	GTEx
rs2304683	XRRA1	cis	lung	GTEx
rs2304683	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs2304683	XRRA1	cis	Adipose Subcutaneous	GTEx
rs2304683	RNF169	cis	lymphoblastoid	seeQTL

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	chr11:74543800-74565800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr11:74544200-74570800	Strong transcription	Duodenum Mucosa	Duodenum
4	chr11:74545600-74564600	Strong transcription	Fetal Muscle Trunk	muscle
5	chr11:74545600-74568400	Strong transcription	Fetal Intestine Large	intestine
6	chr11:74545800-74565000	Strong transcription	Fetal Muscle Leg	muscle
7	chr11:74546000-74566800	Strong transcription	Fetal Stomach	stomach
8	chr11:74547600-74571400	Weak transcription	Fetal Brain Male	brain
9	chr11:74549400-74567600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr11:74550600-74564600	Strong transcription	Fetal Intestine Small	intestine
11	chr11:74551000-74568400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr11:74552600-74565400	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr11:74552800-74576800	Strong transcription	Stomach Smooth Muscle	stomach
14	chr11:74553800-74569400	Weak transcription	Fetal Heart	heart
15	chr11:74554200-74567600	Weak transcription	Psoas Muscle	Psoas
16	chr11:74554800-74571600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:74555800-74569800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr11:74558200-74563400	Strong transcription	Rectal Smooth Muscle	rectum
19	chr11:74558200-74564400	Strong transcription	Thymus	Thymus
20	chr11:74558200-74564600	Strong transcription	Dnd41	blood
21	chr11:74558200-74565200	Strong transcription	Colonic Mucosa	Colon
22	chr11:74558400-74564000	Strong transcription	Fetal Brain Female	brain
23	chr11:74558400-74564200	Strong transcription	Skeletal Muscle Male	skeletal muscle
24	chr11:74558400-74564600	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr11:74558600-74563400	Strong transcription	Brain Anterior Caudate	brain
26	chr11:74558600-74563400	Strong transcription	Left Ventricle	heart
27	chr11:74558600-74563600	Strong transcription	Placenta	Placenta
28	chr11:74558600-74565000	Strong transcription	Primary T cells from cord blood	blood
29	chr11:74558600-74565800	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr11:74558800-74564600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr11:74558800-74565400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr11:74558800-74567400	Weak transcription	Small Intestine	intestine
33	chr11:74559000-74571400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr11:74559200-74565400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr11:74559200-74571400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr11:74559200-74571800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr11:74559400-74570000	Weak transcription	Right Ventricle	heart
38	chr11:74560200-74564800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr11:74560200-74569800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr11:74560400-74564000	Strong transcription	Brain Germinal Matrix	brain
41	chr11:74560400-74565400	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr11:74560600-74563400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr11:74560600-74564800	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr11:74560600-74571200	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr11:74560800-74564600	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr11:74561000-74564200	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr11:74561000-74564600	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr11:74561000-74567800	Weak transcription	Brain Angular Gyrus	brain
49	chr11:74561200-74563400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:74561200-74563400	Strong transcription	A549	lung

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