Variant report

Variant	rs10838660
Chromosome Location	chr11:47152273-47152274
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARFGAP2-1	chr11:47152259-47152352	ENSG00000255520.1

Extended variants
information (count: 110 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10466478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10501319	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs1055447	0.83[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1060573	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769225	0.82[CHB][hapmap]
rs10769226	0.83[CHB][hapmap];0.91[GIH][hapmap]
rs10769227	0.83[CHB][hapmap]
rs10769230	0.83[ASN][1000 genomes]
rs10769233	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10769234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10769239	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10838640	0.83[CHB][hapmap]
rs10838644	0.83[CHB][hapmap];0.91[GIH][hapmap]
rs10838646	0.83[CHB][hapmap]
rs10838652	0.83[CHB][hapmap];0.91[GIH][hapmap]
rs10838654	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10838658	0.82[CHB][hapmap]
rs10838659	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838662	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs10838663	0.83[CHB][hapmap]
rs10838664	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs11039035	0.83[CHB][hapmap]
rs11039074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11039086	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11039097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039107	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039119	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11039124	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11039134	0.87[ASN][1000 genomes]
rs11600292	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs11600668	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11601798	0.85[CHB][hapmap]
rs11602250	0.84[CHB][hapmap]
rs12224096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12291341	0.88[ASN][1000 genomes]
rs12417519	0.83[CHB][hapmap];0.91[GIH][hapmap]
rs12574410	0.86[CHB][hapmap]
rs12796744	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12807887	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17790204	0.82[CHB][hapmap]
rs1872896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965952	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976142	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1976143	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2018527	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029298	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.88[ASN][1000 genomes]
rs2087215	0.83[CHB][hapmap];0.80[CHD][hapmap];0.94[GIH][hapmap]
rs2279438	0.83[CHB][hapmap]
rs2279439	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs4237547	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4319472	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4394802	0.91[GIH][hapmap];0.83[MEX][hapmap]
rs4528282	0.82[CHB][hapmap]
rs4548577	0.83[CHB][hapmap]
rs4567413	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.88[ASN][1000 genomes]
rs4579897	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4581406	0.83[CHB][hapmap];0.91[GIH][hapmap]
rs4587689	0.83[CHB][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap]
rs4752815	0.83[CHB][hapmap];0.91[GIH][hapmap]
rs4752816	0.83[CHB][hapmap];0.91[GIH][hapmap]
rs4752951	0.82[CHB][hapmap]
rs4752952	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4752957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4752962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4752963	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4752965	0.83[CHB][hapmap];0.80[CHD][hapmap]
rs4752967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752969	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs4752971	0.95[CEU][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57323109	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6485715	0.83[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap]
rs6485716	0.86[CHB][hapmap]
rs6485721	0.86[ASN][1000 genomes]
rs6485722	0.85[ASN][1000 genomes]
rs6485726	0.83[CHB][hapmap];0.91[GIH][hapmap]
rs6485739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7103581	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7108902	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7111270	0.83[CHB][hapmap]
rs7111764	0.88[ASN][1000 genomes]
rs7112854	0.82[CHB][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap]
rs7118546	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7119952	0.89[ASN][1000 genomes]
rs7121418	1.00[CEU][hapmap];1.00[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];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7124648	0.83[CHB][hapmap];0.91[GIH][hapmap]
rs7125807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[ASN][1000 genomes]
rs7126005	0.83[CHB][hapmap];0.91[GIH][hapmap]
rs7128325	0.86[ASN][1000 genomes]
rs7128650	0.83[CHB][hapmap];0.91[GIH][hapmap]
rs7130006	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7130947	0.83[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap]
rs747650	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7479189	1.00[CEU][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7931260	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs7935346	0.91[GIH][hapmap]
rs7937101	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7937410	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs7937950	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7938169	0.83[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap]
rs7940240	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs7942473	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7945315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7945558	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs7946709	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7947878	0.82[ASN][1000 genomes]
rs7950753	0.83[CHB][hapmap];0.91[GIH][hapmap]
rs923324	0.82[CHB][hapmap]
rs9633886	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10838660	C11orf49	cis	parietal	SCAN
rs10838660	F2	cis	cerebellum	SCAN
rs10838660	ACP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47124600-47159000	Weak transcription	Primary T cells from cord blood	blood
2	chr11:47129400-47158000	Weak transcription	Aorta	Aorta
3	chr11:47129400-47158600	Weak transcription	Spleen	Spleen
4	chr11:47130000-47159000	Weak transcription	Hela-S3	cervix
5	chr11:47131600-47155000	Weak transcription	Right Atrium	heart
6	chr11:47131600-47159400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:47131800-47161200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr11:47132600-47155600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr11:47140400-47159000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr11:47141000-47159000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr11:47141000-47159400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr11:47141000-47164600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr11:47141200-47154200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr11:47141200-47158400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr11:47141200-47159400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:47143600-47164600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr11:47143600-47175200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr11:47144200-47159400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr11:47145200-47164800	Weak transcription	Ovary	ovary
20	chr11:47145200-47174800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr11:47146000-47159400	Weak transcription	Colon Smooth Muscle	Colon
22	chr11:47146800-47157800	Weak transcription	HSMMtube	muscle
23	chr11:47147000-47158600	Weak transcription	Fetal Lung	lung
24	chr11:47147000-47159200	Weak transcription	Thymus	Thymus
25	chr11:47147600-47164200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr11:47148200-47164400	Weak transcription	NHEK	skin
27	chr11:47148600-47155000	Weak transcription	Small Intestine	intestine
28	chr11:47148800-47153000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr11:47149000-47170400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:47149400-47173200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr11:47149600-47158600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr11:47149600-47170400	Weak transcription	Esophagus	oesophagus
33	chr11:47149800-47164200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr11:47150000-47158600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:47150000-47159200	Weak transcription	Fetal Brain Female	brain
36	chr11:47150400-47153200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr11:47150400-47154800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr11:47150600-47152600	Enhancers	Brain Angular Gyrus	brain
39	chr11:47150800-47155400	Enhancers	Pancreas	Pancrea
40	chr11:47151000-47152800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr11:47151000-47159000	Weak transcription	Brain Hippocampus Middle	brain
42	chr11:47151200-47153000	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr11:47151200-47153600	Weak transcription	Fetal Intestine Small	intestine
44	chr11:47151200-47159200	Weak transcription	Fetal Stomach	stomach
45	chr11:47151200-47159200	Weak transcription	HepG2	liver
46	chr11:47151200-47170600	Weak transcription	Gastric	stomach
47	chr11:47151600-47153000	Enhancers	H1 Cell Line	embryonic stem cell
48	chr11:47151600-47153400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr11:47151800-47152400	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr11:47151800-47152600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell

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