Variant report

Variant	rs1045634
Chromosome Location	chr11:9800450-9800451
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10770061	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10840300	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10840301	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10840302	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840304	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10840307	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11042494	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11042495	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042496	0.90[CEU][hapmap];0.95[EUR][1000 genomes]
rs11042497	0.81[EUR][1000 genomes]
rs11042498	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12786198	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1496475	0.85[JPT][hapmap]
rs1532422	0.84[JPT][hapmap]
rs16907071	0.94[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2878800	0.85[JPT][hapmap]
rs360148	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs360149	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3751001	0.95[ASN][1000 genomes]
rs3763862	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3829252	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910500	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910501	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910502	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910503	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910505	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs55934784	0.97[ASN][1000 genomes]
rs7102804	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7105203	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7113055	0.84[JPT][hapmap]
rs7113459	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7114514	0.84[JPT][hapmap]
rs7120754	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7124706	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7925875	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7936721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9795085	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9795121	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9795122	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9795123	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][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	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking 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	35 gene(s)	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1045634	WEE1	cis	cerebellum	SCAN
rs1045634	OR56A1	cis	cerebellum	SCAN
rs1045634	OR2D2	cis	cerebellum	SCAN
rs1045634	CCKBR	cis	cerebellum	SCAN
rs1045634	OR56B4	cis	cerebellum	SCAN
rs1045634	ASCL3	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9780600-9813200	Weak transcription	Small Intestine	intestine
2	chr11:9781400-9800800	Weak transcription	Fetal Brain Female	brain
3	chr11:9781600-9801000	Weak transcription	Primary T cells from cord blood	blood
4	chr11:9781600-9809000	Weak transcription	Fetal Brain Male	brain
5	chr11:9781800-9801200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr11:9781800-9801600	Weak transcription	Primary B cells from peripheral blood	blood
7	chr11:9784000-9801200	Weak transcription	Gastric	stomach
8	chr11:9787400-9801000	Weak transcription	Aorta	Aorta
9	chr11:9787800-9801000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr11:9787800-9805200	Weak transcription	Colonic Mucosa	Colon
11	chr11:9788000-9801000	Weak transcription	Lung	lung
12	chr11:9788200-9801000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr11:9788600-9801600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:9789200-9801000	Weak transcription	Spleen	Spleen
15	chr11:9791000-9801000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr11:9792000-9801200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr11:9792200-9801000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr11:9793800-9801000	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr11:9794200-9801000	Weak transcription	Fetal Intestine Small	intestine
20	chr11:9795200-9812800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr11:9796600-9801400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr11:9796800-9800800	Weak transcription	HepG2	liver
23	chr11:9796800-9801200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr11:9796800-9803600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr11:9797000-9801000	Weak transcription	Psoas Muscle	Psoas
26	chr11:9797000-9801200	Weak transcription	HUVEC	blood vessel
27	chr11:9797000-9801400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr11:9797200-9800600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr11:9797200-9800800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr11:9797200-9800800	Weak transcription	HMEC	breast
31	chr11:9797200-9801000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr11:9797200-9801000	Weak transcription	Brain Hippocampus Middle	brain
33	chr11:9797200-9801000	Weak transcription	Colon Smooth Muscle	Colon
34	chr11:9797200-9801200	Weak transcription	Pancreas	Pancrea
35	chr11:9797200-9801400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr11:9797200-9801800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr11:9797200-9802000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr11:9797400-9801000	Weak transcription	Brain Anterior Caudate	brain
39	chr11:9797400-9801000	Weak transcription	Brain Substantia Nigra	brain
40	chr11:9797400-9801000	Weak transcription	Esophagus	oesophagus
41	chr11:9797400-9801000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr11:9797400-9801000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr11:9797400-9801200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr11:9797400-9821800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr11:9797600-9800800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr11:9797600-9801000	Weak transcription	Right Ventricle	heart
47	chr11:9797600-9801000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr11:9797600-9801600	Weak transcription	Fetal Thymus	thymus
49	chr11:9797600-9803600	Strong transcription	Fetal Intestine Large	intestine
50	chr11:9797800-9800800	Weak transcription	Dnd41	blood

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