Variant report

Variant	rs12221841
Chromosome Location	chr11:74618701-74618702
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74617868..74619628-chr11:74622578..74625095,2	K562	blood:

Variant related genes	Relation type
ENSG00000241170	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10160410	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10751241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10793105	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10793107	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10793108	0.91[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10899045	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10899051	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10899053	0.92[CEU][hapmap];0.91[JPT][hapmap]
rs10899054	0.81[AMR][1000 genomes]
rs10899058	0.92[CEU][hapmap];0.91[JPT][hapmap]
rs11236244	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11236281	0.87[CEU][hapmap];0.95[JPT][hapmap]
rs11236282	0.91[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes]
rs11236290	0.81[AMR][1000 genomes]
rs11236294	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs11603294	0.90[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes]
rs12223417	0.95[JPT][hapmap]
rs12225372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12225387	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12419113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12419929	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12421899	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12574850	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12575200	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12576129	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]
rs12577127	0.92[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs12577614	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1371410	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs17133461	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]
rs2119028	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2165162	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2165163	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2298746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2304683	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]
rs3814726	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4245440	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs4387374	0.92[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs4483614	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4944061	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]
rs4944947	0.82[JPT][hapmap]
rs4944950	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]
rs4944960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4944961	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4944963	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4944965	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4944968	0.81[AMR][1000 genomes]
rs56194145	0.82[AMR][1000 genomes]
rs59143825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59328242	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61671395	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61734374	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61894779	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61894839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7102619	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7103136	0.91[JPT][hapmap]
rs7105085	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]
rs7128739	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]
rs725460	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7396866	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes]
rs7483351	0.91[CEU][hapmap];0.91[JPT][hapmap]
rs7928381	0.83[EUR][1000 genomes];0.83[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];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9787775	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9787897	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs12221841	XRRA1	cis	Adipose Subcutaneous	GTEx
rs12221841	XRRA1	cis	Esophagus Muscularis	GTEx
rs12221841	XRRA1	cis	Heart Left Ventricle	GTEx
rs12221841	RP11-147I3.1	cis	Thyroid	GTEx
rs12221841	XRRA1	cis	Artery Tibial	GTEx
rs12221841	XRRA1	cis	normal skin	skin_eQTL
rs12221841	XRRA1	cis	Whole Blood	GTEx
rs12221841	XRRA1	cis	lesional skin	skin_eQTL
rs12221841	RP11-147I3.1	cis	Esophagus Muscularis	GTEx
rs12221841	XRRA1	cis	multi-tissue	Pritchard
rs12221841	XRRA1	cis	lung	GTEx
rs12221841	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs12221841	XRRA1	cis	Stomach	GTEx
rs12221841	XRRA1	cis	Esophagus Mucosa	GTEx
rs12221841	XRRA1	cis	Nerve Tibial	GTEx
rs12221841	XRRA1	cis	Thyroid	GTEx
rs12221841	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs12221841	XRRA1	cis	Artery Aorta	GTEx
rs12221841	RP11-147I3.1	cis	Muscle Skeletal	GTEx
rs12221841	XRRA1	cis	Muscle Skeletal	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74587400-74629600	Weak transcription	Gastric	stomach
2	chr11:74588400-74630600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr11:74588400-74636000	Weak transcription	NHLF	lung
4	chr11:74594800-74646600	Weak transcription	Small Intestine	intestine
5	chr11:74596800-74619000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr11:74598400-74629600	Weak transcription	Colon Smooth Muscle	Colon
7	chr11:74599200-74619400	Weak transcription	Colonic Mucosa	Colon
8	chr11:74606600-74626400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr11:74607600-74637400	Weak transcription	Pancreas	Pancrea
10	chr11:74607800-74620800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:74612200-74620600	Weak transcription	HSMM	muscle
12	chr11:74612400-74629600	Weak transcription	NHDF-Ad	bronchial
13	chr11:74612800-74619000	Weak transcription	Brain Angular Gyrus	brain
14	chr11:74612800-74621200	Weak transcription	Fetal Kidney	kidney
15	chr11:74612800-74634000	Weak transcription	Psoas Muscle	Psoas
16	chr11:74613000-74620200	Weak transcription	Fetal Heart	heart
17	chr11:74613400-74621000	Weak transcription	Brain Substantia Nigra	brain
18	chr11:74613400-74632600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr11:74613600-74619200	Weak transcription	Fetal Brain Male	brain
20	chr11:74613600-74624000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr11:74613600-74627800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr11:74613800-74628600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr11:74613800-74637400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr11:74614000-74619200	Weak transcription	Fetal Brain Female	brain
25	chr11:74614200-74620800	Weak transcription	Brain Germinal Matrix	brain
26	chr11:74614400-74618800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:74614400-74623000	Strong transcription	Fetal Intestine Small	intestine
28	chr11:74614600-74633600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr11:74615000-74629600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr11:74615000-74629600	Weak transcription	NH-A	brain
31	chr11:74615000-74636200	Weak transcription	A549	lung
32	chr11:74615200-74619400	Weak transcription	Primary B cells from peripheral blood	blood
33	chr11:74615200-74632600	Strong transcription	Liver	Liver
34	chr11:74615200-74637200	Weak transcription	HMEC	breast
35	chr11:74615400-74623600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr11:74615400-74626400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr11:74615600-74626600	Strong transcription	Dnd41	blood
38	chr11:74615800-74633600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr11:74615800-74644800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr11:74616000-74619200	Strong transcription	Fetal Stomach	stomach
41	chr11:74616000-74621200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr11:74616000-74622800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr11:74616000-74634200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr11:74616000-74634800	Strong transcription	Fetal Intestine Large	intestine
45	chr11:74616200-74626800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr11:74616200-74634000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr11:74616400-74621400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr11:74616400-74622200	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr11:74616400-74623600	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr11:74616400-74633600	Strong transcription	Stomach Smooth Muscle	stomach

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