Variant report

Variant	rs7116459
Chromosome Location	chr11:9275898-9275899
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:9267716..9269230-chr11:9274364..9276054,2	K562	blood:
2	chr11:9267583..9270132-chr11:9274385..9279675,6	K562	blood:
3	chr11:9270425..9272951-chr11:9273779..9275899,2	K562	blood:

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10743105	0.82[CHB][hapmap]
rs10770000	0.81[ASN][1000 genomes]
rs10770001	0.81[ASN][1000 genomes]
rs10770002	0.85[ASN][1000 genomes]
rs10770003	0.85[ASN][1000 genomes]
rs10770004	0.85[ASN][1000 genomes]
rs10770006	0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs10770008	0.95[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs10770009	0.83[ASN][1000 genomes]
rs10770010	0.95[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs10770016	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs10840194	0.82[ASN][1000 genomes]
rs10840196	0.85[ASN][1000 genomes]
rs10840199	0.83[ASN][1000 genomes]
rs10840200	0.83[ASN][1000 genomes]
rs11042227	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11042245	0.96[ASN][1000 genomes]
rs11042252	0.91[ASN][1000 genomes]
rs11042256	0.86[ASN][1000 genomes]
rs11042262	0.83[ASN][1000 genomes]
rs11042264	0.83[ASN][1000 genomes]
rs11042265	0.83[ASN][1000 genomes]
rs11042266	0.82[ASN][1000 genomes]
rs11042267	0.95[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs11042269	0.83[ASN][1000 genomes]
rs11602591	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11608172	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12289113	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12295767	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12296016	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12420463	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12577661	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12796666	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12801814	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2133216	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2873069	0.81[ASN][1000 genomes]
rs34446443	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34494849	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34716494	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34729888	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35381016	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35686957	0.86[ASN][1000 genomes]
rs35757766	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35955530	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4343026	0.82[ASN][1000 genomes]
rs4369406	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4447178	0.85[ASN][1000 genomes]
rs4601779	0.84[ASN][1000 genomes]
rs5014247	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs61875672	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61875673	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61877814	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61877916	0.87[ASN][1000 genomes]
rs6486206	0.90[JPT][hapmap]
rs6486210	0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs6486226	0.84[ASN][1000 genomes]
rs6486231	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7101432	0.86[ASN][1000 genomes]
rs7104221	0.93[ASW][hapmap];0.90[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7112540	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7114688	0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs7115062	0.84[ASN][1000 genomes]
rs7121013	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs7123342	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7124178	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71476818	0.85[ASN][1000 genomes]
rs7358313	0.83[ASN][1000 genomes]
rs7396439	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs770	0.81[ASN][1000 genomes]
rs7924664	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7933448	0.81[ASN][1000 genomes]
rs7941520	0.81[ASN][1000 genomes]
rs7951700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7952508	0.82[ASN][1000 genomes]
rs952374	0.90[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs956517	0.92[YRI][hapmap]
rs9736263	0.81[ASN][1000 genomes]
rs9888193	1.00[ASW][hapmap];0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9888229	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
4	nsv916534	chr11:9188436-9516241	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv1053045	chr11:9208881-9363488	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv540947	chr11:9208881-9363488	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv1055078	chr11:9252857-9538877	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
8	nsv515891	chr11:9275898-9334961	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7116459	CCKBR	cis	cerebellum	SCAN
rs7116459	DNHD1	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9253000-9285600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:9254400-9280600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr11:9257000-9276000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr11:9257000-9284800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr11:9257200-9285600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:9257600-9276800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr11:9261800-9285600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:9262400-9282400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr11:9264000-9276800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr11:9264000-9283400	Weak transcription	Fetal Lung	lung
11	chr11:9264000-9284600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr11:9264200-9285400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr11:9265200-9279400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr11:9265600-9284600	Weak transcription	Brain Germinal Matrix	brain
15	chr11:9267200-9276200	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr11:9267800-9285600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr11:9269400-9280000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr11:9270200-9282000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr11:9270200-9284800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:9271800-9280200	Weak transcription	HSMM	muscle
21	chr11:9272000-9278000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr11:9272000-9282000	Weak transcription	NHDF-Ad	bronchial
23	chr11:9272000-9284600	Weak transcription	Fetal Brain Female	brain
24	chr11:9272000-9285400	Weak transcription	HSMMtube	muscle
25	chr11:9272200-9276200	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr11:9272200-9279800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:9272200-9281600	Weak transcription	Hela-S3	cervix
28	chr11:9272200-9281600	Weak transcription	Osteobl	bone
29	chr11:9272400-9281600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr11:9272400-9282000	Weak transcription	NHLF	lung
31	chr11:9272400-9282800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr11:9272600-9281200	Weak transcription	Right Ventricle	heart
33	chr11:9272600-9281400	Weak transcription	Ovary	ovary
34	chr11:9272600-9281400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr11:9272600-9285600	Weak transcription	Small Intestine	intestine
36	chr11:9272800-9278000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr11:9273200-9276400	Enhancers	Primary T cells from cord blood	blood
38	chr11:9273200-9276600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr11:9273200-9276600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr11:9273200-9278200	Weak transcription	A549	lung
41	chr11:9273200-9282600	Weak transcription	Thymus	Thymus
42	chr11:9273200-9285400	Weak transcription	K562	blood
43	chr11:9273400-9278200	Weak transcription	NHEK	skin
44	chr11:9273400-9280000	Weak transcription	GM12878-XiMat	blood
45	chr11:9273400-9281200	Weak transcription	Primary B cells from cord blood	blood
46	chr11:9273600-9276800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr11:9273600-9278400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr11:9274000-9278600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:9274400-9277600	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr11:9274400-9277600	Strong transcription	Fetal Muscle Leg	muscle

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