Variant report

Variant	rs232054
Chromosome Location	chr11:4123427-4123428
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	chr11:4114277..4116935-chr11:4123036..4125551,3	K562	blood:

Variant related genes	Relation type
ENSG00000167325	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1015998	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10835613	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10835650	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11030842	0.90[CHB][hapmap]
rs11030976	0.83[AMR][1000 genomes]
rs11030980	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11031043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11031062	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11031070	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1372804	0.90[CHB][hapmap]
rs1662161	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1662173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs183484	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1980412	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2284452	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2735689	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2735691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2923945	0.81[CHB][hapmap]
rs2959056	0.86[CHB][hapmap]
rs2959070	0.86[CHB][hapmap]
rs2959075	0.85[CHB][hapmap]
rs34356743	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3794049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4910913	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4910914	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs54816	0.83[AMR][1000 genomes]
rs9937	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv896896	chr11:4010409-4185595	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2758253	chr11:4055945-4510188	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	esv2759797	chr11:4055945-4510188	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv428248	chr11:4055945-4510188	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv832053	chr11:4096527-4330263	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1053189	chr11:4123119-4359044	Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs232054	CHRNA10	cis	Artery Tibial	GTEx
rs232054	RRM1	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4117000-4124600	Weak transcription	Aorta	Aorta
2	chr11:4117000-4124600	Weak transcription	Left Ventricle	heart
3	chr11:4117000-4137200	Weak transcription	Esophagus	oesophagus
4	chr11:4117000-4141000	Weak transcription	Ovary	ovary
5	chr11:4117200-4126800	Weak transcription	Psoas Muscle	Psoas
6	chr11:4117200-4127400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr11:4117200-4142200	Weak transcription	Colonic Mucosa	Colon
8	chr11:4117400-4124200	Weak transcription	Brain Anterior Caudate	brain
9	chr11:4117400-4124600	Weak transcription	Lung	lung
10	chr11:4117400-4124600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr11:4117400-4125800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:4117400-4141800	Weak transcription	Small Intestine	intestine
13	chr11:4117600-4123800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr11:4117600-4124000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr11:4117600-4124000	Weak transcription	Fetal Muscle Leg	muscle
16	chr11:4117600-4124200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr11:4117600-4124600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr11:4117600-4124800	Weak transcription	Fetal Intestine Small	intestine
19	chr11:4117600-4125200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr11:4117600-4125800	Weak transcription	Liver	Liver
21	chr11:4117600-4126400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr11:4117600-4126400	Weak transcription	Fetal Intestine Large	intestine
23	chr11:4117600-4126600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr11:4117600-4126600	Weak transcription	Spleen	Spleen
25	chr11:4117600-4127000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr11:4117600-4127000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr11:4117600-4127200	Weak transcription	Brain Hippocampus Middle	brain
28	chr11:4117600-4127200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr11:4117600-4128600	Weak transcription	Brain Substantia Nigra	brain
30	chr11:4117600-4129200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr11:4117600-4129800	Weak transcription	Fetal Heart	heart
32	chr11:4117600-4133000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr11:4117600-4137400	Weak transcription	Right Ventricle	heart
34	chr11:4117600-4144600	Weak transcription	HSMMtube	muscle
35	chr11:4117600-4145200	Weak transcription	Gastric	stomach
36	chr11:4117600-4153000	Weak transcription	Stomach Mucosa	stomach
37	chr11:4117800-4124000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr11:4117800-4124200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr11:4117800-4124800	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr11:4117800-4126400	Weak transcription	Brain Angular Gyrus	brain
41	chr11:4117800-4126400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr11:4117800-4126800	Weak transcription	NHLF	lung
43	chr11:4117800-4127000	Weak transcription	Colon Smooth Muscle	Colon
44	chr11:4117800-4147800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr11:4117800-4160200	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr11:4118000-4123800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr11:4118000-4125200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr11:4118000-4159200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr11:4118400-4123800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr11:4118400-4123800	Weak transcription	HMEC	breast

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