Variant report

Variant	rs7120754
Chromosome Location	chr11:9798736-9798737
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1045634	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[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]
rs1056593	0.80[JPT][hapmap]
rs10770061	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10840300	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10840301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10840302	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10840304	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10840307	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11042494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11042495	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11042496	0.90[CEU][hapmap];0.95[EUR][1000 genomes]
rs11042497	0.80[EUR][1000 genomes]
rs11042498	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.94[ASN][1000 genomes]
rs12786198	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1496475	0.85[JPT][hapmap]
rs1532422	0.85[JPT][hapmap]
rs16907071	0.94[CHB][hapmap];0.90[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];0.97[ASN][1000 genomes]
rs360149	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3751001	0.95[ASN][1000 genomes]
rs3763862	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3829252	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910500	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4910501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4910502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4910503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4910505	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs55934784	0.96[ASN][1000 genomes]
rs7102804	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7105203	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7113055	0.84[JPT][hapmap]
rs7113459	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7114514	0.84[JPT][hapmap]
rs7124706	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7925875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7936721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9795085	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9795121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9795122	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9795123	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[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
rs7120754	ASCL3	cis	parietal	SCAN
rs7120754	OR2D2	cis	cerebellum	SCAN
rs7120754	OR56B4	cis	cerebellum	SCAN
rs7120754	WEE1	cis	cerebellum	SCAN
rs7120754	CCKBR	cis	cerebellum	SCAN
rs7120754	OR56A1	cis	cerebellum	SCAN

Chromatin state (count:115 , 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	chr11:9781800-9799200	Weak transcription	Primary B cells from cord blood	blood
6	chr11:9781800-9799200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr11:9781800-9801200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr11:9781800-9801600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr11:9782400-9799400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr11:9784000-9801200	Weak transcription	Gastric	stomach
11	chr11:9787400-9799000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr11:9787400-9801000	Weak transcription	Aorta	Aorta
13	chr11:9787600-9799200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr11:9787600-9799200	Weak transcription	Fetal Lung	lung
15	chr11:9787800-9801000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr11:9787800-9805200	Weak transcription	Colonic Mucosa	Colon
17	chr11:9788000-9801000	Weak transcription	Lung	lung
18	chr11:9788200-9801000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr11:9788600-9801600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:9788800-9799000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:9789200-9801000	Weak transcription	Spleen	Spleen
22	chr11:9790200-9799200	Weak transcription	Adipose Nuclei	Adipose
23	chr11:9791000-9801000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr11:9792000-9801200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr11:9792200-9801000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr11:9792600-9798800	Weak transcription	Brain Germinal Matrix	brain
27	chr11:9792600-9799000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr11:9793800-9801000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr11:9794200-9801000	Weak transcription	Fetal Intestine Small	intestine
30	chr11:9795200-9812800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr11:9795400-9798800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr11:9795400-9798800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr11:9795600-9799000	Weak transcription	Fetal Stomach	stomach
34	chr11:9795800-9799000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr11:9796200-9799600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr11:9796400-9799000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr11:9796400-9799200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:9796400-9799200	Weak transcription	Fetal Kidney	kidney
39	chr11:9796400-9799600	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr11:9796400-9799600	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr11:9796400-9799600	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr11:9796600-9799000	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr11:9796600-9799400	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr11:9796600-9801400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr11:9796800-9799200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr11:9796800-9800800	Weak transcription	HepG2	liver
47	chr11:9796800-9801200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr11:9796800-9803600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr11:9797000-9799600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr11:9797000-9799800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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