Variant report

Variant	rs10840176
Chromosome Location	chr11:9155570-9155571
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:9151966..9154190-chr11:9155190..9157192,2	K562	blood:
2	chr11:9149953..9152541-chr11:9155189..9157810,2	K562	blood:
3	chr11:9022966..9025427-chr11:9154942..9157918,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10047438	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1039210	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10769991	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10769992	0.88[CEU][hapmap];0.83[JPT][hapmap];0.81[YRI][hapmap]
rs10769994	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10769995	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10769996	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10769997	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10769998	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10770006	0.83[YRI][hapmap]
rs10770008	0.83[YRI][hapmap]
rs10770010	0.83[YRI][hapmap]
rs10840175	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10840178	0.98[ASN][1000 genomes]
rs10840179	1.00[ASN][1000 genomes]
rs10840181	0.82[ASN][1000 genomes]
rs10840182	0.82[ASN][1000 genomes]
rs10840183	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10840185	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11042189	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11042195	0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11042199	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs11042200	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11604616	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs12291375	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17256375	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1827011	0.92[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1874822	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997628	0.91[ASN][1000 genomes]
rs2133217	0.88[CEU][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2291839	0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs2316087	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2647533	0.88[CEU][hapmap]
rs2647537	0.92[CEU][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2742556	0.81[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2742557	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4910035	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5011703	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56077948	0.82[ASN][1000 genomes]
rs56216908	0.92[ASN][1000 genomes]
rs7109745	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7120239	0.82[EUR][1000 genomes]
rs7123970	0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7128469	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7394878	0.80[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap]
rs7395151	0.84[CEU][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7395347	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7395846	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7396705	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7925308	0.86[CHB][hapmap]
rs7930507	0.80[CEU][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.81[EUR][1000 genomes]
rs7931872	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7947251	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9888257	0.92[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040049	chr11:9152536-9363488	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10840176	TMEM41B	cis	multi-tissue	Pritchard
rs10840176	TRIM5	cis	cerebellum	SCAN
rs10840176	EIF4G2	cis	cerebellum	SCAN
rs10840176	OR56A1	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9113600-9159800	Weak transcription	Right Ventricle	heart
2	chr11:9134800-9159000	Weak transcription	Brain Hippocampus Middle	brain
3	chr11:9134800-9161200	Weak transcription	Fetal Brain Male	brain
4	chr11:9136400-9159200	Weak transcription	Brain Anterior Caudate	brain
5	chr11:9137200-9159000	Weak transcription	Fetal Heart	heart
6	chr11:9141600-9158400	Weak transcription	Pancreas	Pancrea
7	chr11:9142000-9157200	Weak transcription	NHLF	lung
8	chr11:9142400-9163000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr11:9142600-9159000	Weak transcription	Adipose Nuclei	Adipose
10	chr11:9142600-9159200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr11:9142600-9175000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr11:9143400-9159200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:9143400-9161200	Weak transcription	Aorta	Aorta
14	chr11:9143600-9159000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr11:9143800-9158800	Weak transcription	Fetal Brain Female	brain
16	chr11:9144400-9161200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr11:9145400-9156800	Weak transcription	Placenta	Placenta
18	chr11:9146000-9157400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr11:9146400-9158400	Weak transcription	Gastric	stomach
20	chr11:9146400-9159200	Weak transcription	K562	blood
21	chr11:9146600-9158800	Weak transcription	Lung	lung
22	chr11:9147000-9158800	Weak transcription	A549	lung
23	chr11:9148400-9158400	Weak transcription	GM12878-XiMat	blood
24	chr11:9148400-9159000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr11:9148400-9159000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr11:9148400-9159200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr11:9148600-9159000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr11:9148800-9158000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr11:9148800-9159000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr11:9149000-9158800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:9149400-9157800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr11:9149800-9157400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr11:9150600-9160000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr11:9151400-9155600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr11:9151600-9158400	Weak transcription	HSMMtube	muscle
36	chr11:9151800-9155600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr11:9151800-9159000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr11:9151800-9160800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:9151800-9175800	Strong transcription	Fetal Muscle Trunk	muscle
40	chr11:9152000-9157800	Strong transcription	Fetal Stomach	stomach
41	chr11:9152000-9158800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr11:9152000-9159800	Weak transcription	Liver	Liver
43	chr11:9152200-9160600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:9152400-9157000	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr11:9152400-9158400	Weak transcription	Thymus	Thymus
46	chr11:9152400-9159000	Weak transcription	Fetal Intestine Small	intestine
47	chr11:9152400-9159000	Weak transcription	Hela-S3	cervix
48	chr11:9152600-9157800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:9152600-9158400	Weak transcription	Fetal Thymus	thymus
50	chr11:9152600-9158800	Weak transcription	Fetal Lung	lung

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