Variant report

Variant	rs10840311
Chromosome Location	chr11:9854857-9854858
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10743119	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10770067	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10770068	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11601110	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12273851	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12278797	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12574461	0.83[ASN][1000 genomes]
rs12574467	0.81[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs12574474	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12574508	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12574765	0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12575022	0.82[ASN][1000 genomes]
rs12576762	0.90[ASN][1000 genomes]
rs12576763	0.83[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12577960	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12578023	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17268414	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2403221	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2403222	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs360118	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7108907	0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7937716	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7948674	0.82[ASN][1000 genomes]
rs7951573	0.88[ASN][1000 genomes]
rs958875	0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv896987	chr11:9759918-9885849	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	esv3384280	chr11:9766350-9911228	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	esv2762895	chr11:9849511-9954549	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10840311	PPFIBP2	cis	parietal	SCAN
rs10840311	CYB5R2	cis	cerebellum	SCAN
rs10840311	SNORA23	cis	cerebellum	SCAN
rs10840311	SNORA23	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9812200-9862200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr11:9818600-9881400	Weak transcription	Spleen	Spleen
3	chr11:9824200-9867600	Weak transcription	Psoas Muscle	Psoas
4	chr11:9826800-9868200	Weak transcription	Aorta	Aorta
5	chr11:9829600-9865600	Weak transcription	Gastric	stomach
6	chr11:9830000-9860000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:9830000-9860800	Weak transcription	Primary T cells from cord blood	blood
8	chr11:9830000-9864400	Weak transcription	Esophagus	oesophagus
9	chr11:9830200-9863000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr11:9830400-9860400	Weak transcription	Primary B cells from cord blood	blood
11	chr11:9830400-9860400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr11:9830400-9860400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr11:9830400-9860400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr11:9830400-9860800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr11:9830400-9880400	Weak transcription	Thymus	Thymus
16	chr11:9830600-9860400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr11:9830800-9860600	Weak transcription	Colon Smooth Muscle	Colon
18	chr11:9830800-9865600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr11:9830800-9866800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr11:9830800-9880600	Weak transcription	Fetal Brain Male	brain
21	chr11:9833400-9868400	Weak transcription	Fetal Kidney	kidney
22	chr11:9833600-9878800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr11:9834200-9876600	Weak transcription	Brain Germinal Matrix	brain
24	chr11:9834400-9860600	Weak transcription	Brain Anterior Caudate	brain
25	chr11:9834600-9856000	Weak transcription	Fetal Brain Female	brain
26	chr11:9834600-9867400	Weak transcription	Brain Hippocampus Middle	brain
27	chr11:9834600-9877200	Weak transcription	Right Ventricle	heart
28	chr11:9835400-9860400	Weak transcription	Fetal Stomach	stomach
29	chr11:9837600-9860400	Weak transcription	HSMMtube	muscle
30	chr11:9837600-9863200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr11:9837600-9885800	Weak transcription	Hela-S3	cervix
32	chr11:9838000-9859200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr11:9838600-9879800	Weak transcription	Fetal Thymus	thymus
34	chr11:9842000-9856400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr11:9843200-9859800	Weak transcription	NH-A	brain
36	chr11:9843600-9859800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr11:9845000-9860200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr11:9845400-9860000	Weak transcription	HMEC	breast
39	chr11:9845400-9860400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr11:9845400-9860600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr11:9845800-9860400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr11:9847600-9859600	Weak transcription	NHEK	skin
43	chr11:9848200-9877000	Weak transcription	HepG2	liver
44	chr11:9849000-9860600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr11:9849000-9863000	Weak transcription	Ovary	ovary
46	chr11:9850200-9856200	Weak transcription	NHDF-Ad	bronchial
47	chr11:9850200-9856400	Weak transcription	Pancreas	Pancrea
48	chr11:9850200-9859600	Weak transcription	HSMM	muscle
49	chr11:9850400-9856000	Weak transcription	Fetal Heart	heart
50	chr11:9851200-9880000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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