Variant report

Variant	rs2904967
Chromosome Location	chr11:65091609-65091610
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1152611	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1195733	0.90[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12269727	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1633466	0.90[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes]
rs1783486	1.00[ASW][hapmap];0.90[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap]
rs1858783	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs239261	0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap]
rs28781278	0.91[EUR][1000 genomes]
rs2904966	1.00[CHB][hapmap];0.88[GIH][hapmap];0.83[ASN][1000 genomes]
rs2904979	0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap]
rs2904980	0.90[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs2904982	1.00[CHB][hapmap]
rs2904984	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs2904986	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3015997	0.89[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap]
rs3016000	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3741386	1.00[CHB][hapmap]
rs4149813	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs482842	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs487568	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs487989	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs488289	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs499027	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs503277	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507005	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs509303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs526502	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs542142	0.83[ASN][1000 genomes]
rs551523	1.00[CHB][hapmap]
rs554122	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs560097	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs592050	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs603286	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs611910	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs612392	0.83[CHD][hapmap];0.86[MEX][hapmap]
rs620427	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.86[MEX][hapmap]
rs626555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs626802	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs630055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636928	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs655433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs667341	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs668735	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs673147	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs676114	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.86[MEX][hapmap];0.83[ASN][1000 genomes]
rs676573	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs689288	0.83[CHD][hapmap];0.86[MEX][hapmap]
rs7116674	0.94[CHD][hapmap]
rs8638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv832190	chr11:64978144-65127613	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	esv2422285	chr11:65013294-65254540	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases
4	nsv897714	chr11:65076918-65091609	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
6	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2904967	EFEMP2	cis	cerebellum	SCAN
rs2904967	POLA2	cis	parietal	SCAN
rs2904967	BANF1	cis	parietal	SCAN
rs2904967	BATF2	cis	cerebellum	SCAN
rs2904967	POLA2	cis	lymphoblastoid	seeQTL
rs2904967	SNORD27	cis	parietal	SCAN
rs2904967	PLCB3	cis	cerebellum	SCAN
rs2904967	POLA2	Cis_1M	lymphoblastoid	RTeQTL
rs2904967	RPS6KB2	cis	cerebellum	SCAN
rs2904967	GAL3ST3	cis	cerebellum	SCAN
rs2904967	POLA2	cis	multi-tissue	Pritchard

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65083200-65093400	Weak transcription	Aorta	Aorta
2	chr11:65083600-65096600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr11:65083800-65096600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr11:65085000-65100800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:65085200-65097200	Weak transcription	Stomach Mucosa	stomach
6	chr11:65085200-65101000	Weak transcription	Fetal Kidney	kidney
7	chr11:65085400-65097000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:65085800-65091800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr11:65085800-65101000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr11:65086200-65092200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:65086800-65092000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr11:65088800-65101000	Weak transcription	Right Atrium	heart
13	chr11:65089200-65101000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr11:65089400-65101200	Weak transcription	Small Intestine	intestine
15	chr11:65089600-65096800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr11:65089800-65091800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:65089800-65092600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr11:65089800-65094800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr11:65089800-65097400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:65089800-65100800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr11:65089800-65101000	Weak transcription	Liver	Liver
22	chr11:65089800-65101000	Weak transcription	Esophagus	oesophagus
23	chr11:65090000-65091800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr11:65090000-65095800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr11:65090000-65096800	Weak transcription	HepG2	liver
26	chr11:65090000-65097000	Weak transcription	Brain Anterior Caudate	brain
27	chr11:65090000-65097200	Weak transcription	Brain Angular Gyrus	brain
28	chr11:65090000-65097200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr11:65090000-65101000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr11:65090000-65101000	Weak transcription	Brain Substantia Nigra	brain
31	chr11:65090000-65101000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr11:65090200-65091800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr11:65090200-65091800	Strong transcription	NHLF	lung
34	chr11:65090200-65096600	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr11:65090200-65096800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:65090200-65097000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr11:65090200-65097000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:65090200-65097000	Weak transcription	Colon Smooth Muscle	Colon
39	chr11:65090200-65097000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr11:65090200-65097200	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr11:65090200-65097200	Weak transcription	Brain Hippocampus Middle	brain
42	chr11:65090200-65097200	Weak transcription	Fetal Brain Female	brain
43	chr11:65090200-65097400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr11:65090200-65100800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr11:65090200-65100800	Weak transcription	Colonic Mucosa	Colon
46	chr11:65090200-65101000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr11:65090200-65101000	Weak transcription	Fetal Lung	lung
48	chr11:65090200-65101000	Weak transcription	Rectal Smooth Muscle	rectum
49	chr11:65090400-65092200	Strong transcription	Fetal Muscle Leg	muscle
50	chr11:65090400-65094000	Weak transcription	H1 Cell Line	embryonic stem cell

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