Variant report

Variant	rs7945831
Chromosome Location	chr11:36455749-36455750
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10768210	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10836559	0.85[CHB][hapmap]
rs10836560	0.94[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10836561	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11033617	0.87[ASW][hapmap];0.95[CEU][hapmap];0.82[CHD][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11033619	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12223629	0.90[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.86[ASN][1000 genomes]
rs12793521	0.95[CEU][hapmap];0.82[CHD][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs1863397	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2422251	0.85[CHB][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs331446	0.84[LWK][hapmap];0.80[MKK][hapmap]
rs577054	0.88[MEX][hapmap];0.82[YRI][hapmap]
rs744895	1.00[ASW][hapmap];0.81[CHB][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs744896	1.00[ASW][hapmap];0.81[CHB][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes]
rs746762	0.87[ASW][hapmap];0.85[CHB][hapmap];0.81[MKK][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs750940	0.80[CHB][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs754005	0.94[ASW][hapmap];0.81[CHB][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs7951020	0.86[YRI][hapmap]
rs7952013	0.84[CHB][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467791	chr11:36108497-36999385	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv554003	chr11:36108497-36999385	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv2762906	chr11:36453831-36457253	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7945831	PAMR1	cis	cerebellum	SCAN
rs7945831	ATP2C1	trans	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:36400200-36475400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:36413000-36471000	Weak transcription	Aorta	Aorta
3	chr11:36414800-36475600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr11:36432000-36467800	Weak transcription	Esophagus	oesophagus
5	chr11:36433800-36471400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr11:36435200-36463200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr11:36442600-36462200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:36443800-36457400	Weak transcription	Colon Smooth Muscle	Colon
9	chr11:36444000-36471400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr11:36444200-36471400	Weak transcription	Small Intestine	intestine
11	chr11:36447600-36471000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr11:36448400-36463800	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr11:36448400-36470600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr11:36448600-36470600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr11:36448600-36471000	Weak transcription	Fetal Thymus	thymus
16	chr11:36448600-36471000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr11:36448800-36463000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr11:36448800-36471400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr11:36449200-36467800	Weak transcription	Ovary	ovary
20	chr11:36449200-36469200	Weak transcription	Placenta	Placenta
21	chr11:36449200-36471400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr11:36449400-36457800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr11:36449400-36471200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr11:36449400-36471200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr11:36449600-36457000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr11:36449600-36463000	Weak transcription	Fetal Muscle Leg	muscle
27	chr11:36449600-36467600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr11:36449600-36469000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr11:36449600-36474000	Weak transcription	Right Ventricle	heart
30	chr11:36449800-36460400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr11:36449800-36463000	Weak transcription	Fetal Stomach	stomach
32	chr11:36449800-36463000	Weak transcription	Lung	lung
33	chr11:36450000-36468400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr11:36450200-36459000	Weak transcription	Gastric	stomach
35	chr11:36450200-36463400	Weak transcription	Brain Anterior Caudate	brain
36	chr11:36451800-36460600	Weak transcription	Pancreas	Pancrea
37	chr11:36452400-36470600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr11:36452800-36473800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr11:36453000-36456600	Genic enhancers	Fetal Intestine Large	intestine
40	chr11:36453200-36462600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr11:36453400-36456400	Weak transcription	Spleen	Spleen
42	chr11:36453400-36464400	Weak transcription	Brain Angular Gyrus	brain
43	chr11:36453400-36471200	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr11:36453600-36456800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr11:36453600-36457800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr11:36453600-36458800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr11:36453600-36460600	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr11:36453600-36461200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr11:36453600-36463000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:36453600-36471200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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