Variant report

Variant	rs12577127
Chromosome Location	chr11:74714008-74714009
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74709211..74711419-chr11:74713806..74715440,2	K562	blood:
2	chr11:74698514..74700632-chr11:74711849..74715007,3	K562	blood:
3	chr11:74674114..74677070-chr11:74712523..74714236,2	K562	blood:
4	chr11:74709502..74714442-chr11:74716351..74722182,6	K562	blood:

Variant related genes	Relation type
ENSG00000162139	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 29 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10751241	0.91[CEU][hapmap];0.95[JPT][hapmap]
rs10793107	0.95[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10793108	0.91[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10793112	0.81[AMR][1000 genomes]
rs10899051	0.83[AMR][1000 genomes]
rs10899052	0.91[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes]
rs10899053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899054	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899058	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899059	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10899060	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10899061	0.81[AMR][1000 genomes]
rs11236281	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236289	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11236290	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11236294	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11236296	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11236306	0.86[AFR][1000 genomes]
rs11603294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12221841	0.92[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs12225372	0.81[AMR][1000 genomes]
rs12419113	0.81[AMR][1000 genomes]
rs12419929	0.81[AMR][1000 genomes]
rs12575200	0.81[AMR][1000 genomes]
rs12577614	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1371410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2119028	0.96[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2165162	0.96[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2165163	0.96[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2298746	0.92[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs2304683	0.92[CEU][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs3814726	0.86[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap]
rs4245440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4387374	1.00[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];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4456280	0.90[GIH][hapmap]
rs4483614	0.92[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap]
rs4944960	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs4944961	0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap]
rs4944965	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944970	0.81[AMR][1000 genomes]
rs56194145	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59143825	0.81[AMR][1000 genomes]
rs61671395	0.81[AMR][1000 genomes]
rs61894839	0.81[AMR][1000 genomes]
rs7102619	0.82[AMR][1000 genomes]
rs7105085	0.91[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs7106757	0.81[AMR][1000 genomes]
rs7128739	0.92[CEU][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs725460	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7396866	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7483351	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs919877	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs9787775	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9787897	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:29)

SNP	Gene	Cis/trans	Tissue	Source
rs12577127	XRRA1	cis	Adipose Subcutaneous	GTEx
rs12577127	XRRA1	cis	lesional skin	skin_eQTL
rs12577127	PAAF1	cis	parietal	SCAN
rs12577127	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs12577127	PLEKHB1	cis	cerebellum	SCAN
rs12577127	XRRA1	cis	Whole Blood	GTEx
rs12577127	XRRA1	cis	Nerve Tibial	GTEx
rs12577127	XRRA1	cis	multi-tissue	Pritchard
rs12577127	XRRA1	cis	cerebellum	SCAN
rs12577127	XRRA1	cis	lymphoblastoid	seeQTL
rs12577127	XRRA1	cis	Thyroid	GTEx
rs12577127	XRRA1	cis	Esophagus Muscularis	GTEx
rs12577127	XRRA1	cis	Artery Tibial	GTEx
rs12577127	XRRA1	cis	normal skin	skin_eQTL
rs12577127	RP11-147I3.1	cis	Esophagus Muscularis	GTEx
rs12577127	XRRA1	cis	Heart Left Ventricle	GTEx
rs12577127	XRRA1	cis	lung	GTEx
rs12577127	RNF169	cis	lymphoblastoid	seeQTL
rs12577127	XRRA1	cis	parietal	SCAN
rs12577127	RP11-147I3.1	cis	Thyroid	GTEx
rs12577127	RP11-147I3.1	cis	Muscle Skeletal	GTEx
rs12577127	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs12577127	XRRA1	cis	Muscle Skeletal	GTEx
rs12577127	RNF169	cis	multi-tissue	Pritchard
rs12577127	XRRA1	cis	lymphoblastoid	GTEx
rs12577127	XRRA1	cis	Artery Aorta	GTEx
rs12577127	RNF169	cis	cerebellum	SCAN
rs12577127	XRRA1	cis	Esophagus Mucosa	GTEx
rs12577127	XRRA1	cis	Stomach	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74700400-74716400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:74700400-74723000	Weak transcription	Small Intestine	intestine
3	chr11:74700600-74716400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:74700600-74716400	Weak transcription	Aorta	Aorta
5	chr11:74700600-74716400	Weak transcription	Esophagus	oesophagus
6	chr11:74700600-74716400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:74700600-74716600	Weak transcription	Fetal Brain Male	brain
8	chr11:74700600-74722600	Weak transcription	HSMM	muscle
9	chr11:74700600-74725000	Weak transcription	HSMMtube	muscle
10	chr11:74700800-74716400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr11:74700800-74716400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr11:74700800-74716400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr11:74700800-74716400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr11:74700800-74716400	Weak transcription	NHLF	lung
15	chr11:74700800-74716600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:74701000-74716400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr11:74701000-74716400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr11:74701000-74716400	Weak transcription	Colonic Mucosa	Colon
19	chr11:74701000-74716600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:74701000-74716600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr11:74701000-74716600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr11:74701000-74716600	Weak transcription	Colon Smooth Muscle	Colon
23	chr11:74701000-74716600	Weak transcription	NH-A	brain
24	chr11:74701000-74722000	Weak transcription	Fetal Kidney	kidney
25	chr11:74701000-74722600	Weak transcription	HUVEC	blood vessel
26	chr11:74701000-74723800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr11:74701200-74716400	Weak transcription	A549	lung
28	chr11:74701400-74716400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr11:74701600-74721600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr11:74701800-74716600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr11:74702400-74716600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr11:74702400-74716600	Weak transcription	Fetal Heart	heart
33	chr11:74702400-74722800	Weak transcription	Stomach Mucosa	stomach
34	chr11:74702800-74716400	Weak transcription	Pancreas	Pancrea
35	chr11:74702800-74717600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr11:74703200-74720600	Weak transcription	Psoas Muscle	Psoas
37	chr11:74705800-74716400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr11:74706000-74716600	Weak transcription	Brain Hippocampus Middle	brain
39	chr11:74706200-74716400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr11:74706400-74715400	Weak transcription	Hela-S3	cervix
41	chr11:74706400-74716400	Weak transcription	Brain Angular Gyrus	brain
42	chr11:74706400-74716400	Weak transcription	Fetal Brain Female	brain
43	chr11:74706400-74716400	Weak transcription	Gastric	stomach
44	chr11:74706400-74716400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr11:74706400-74716600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr11:74706400-74716600	Weak transcription	HMEC	breast
47	chr11:74706600-74715400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr11:74706600-74716200	Weak transcription	HepG2	liver
49	chr11:74706600-74716200	Weak transcription	NHEK	skin
50	chr11:74706600-74716400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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