Variant report

Variant	rs2304891
Chromosome Location	chr11:4103524-4103525
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr11:4103426-4103606	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
STIM1	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10742189	0.81[GIH][hapmap]
rs10742223	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10767807	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10835613	0.85[ASW][hapmap];0.85[CEU][hapmap];0.88[CHD][hapmap];0.84[MEX][hapmap]
rs10835650	0.80[EUR][1000 genomes]
rs11030394	0.89[AFR][1000 genomes]
rs11030536	0.87[AFR][1000 genomes]
rs11030841	0.83[MKK][hapmap]
rs11030853	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11030907	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11030976	0.81[ASW][hapmap];0.82[CEU][hapmap];0.88[CHD][hapmap];0.83[MEX][hapmap];0.81[EUR][1000 genomes]
rs11604649	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12294167	0.88[YRI][hapmap]
rs12364664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12419208	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12799265	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12803023	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1372805	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1662172	0.82[CEU][hapmap];0.82[CHD][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs2119986	0.80[EUR][1000 genomes]
rs2412344	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2920139	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2920143	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2920144	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2923944	0.93[ASW][hapmap];1.00[LWK][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes]
rs2923950	0.80[EUR][1000 genomes]
rs2923953	0.92[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2923956	0.85[ASW][hapmap];0.87[GIH][hapmap];0.85[MKK][hapmap]
rs2958713	0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs2958714	0.93[ASW][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes]
rs2959066	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2959068	0.93[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2959074	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2959079	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2959081	0.85[ASW][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap]
rs54816	0.82[CEU][hapmap]
rs61188043	0.81[AFR][1000 genomes]
rs7102508	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7110060	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7116520	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7124301	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs725518	0.85[CEU][hapmap];0.88[CHD][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs725519	0.82[CEU][hapmap];0.88[CHD][hapmap];0.84[MEX][hapmap];0.80[EUR][1000 genomes]
rs747883	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7933164	0.88[MKK][hapmap]
rs7945639	0.83[MKK][hapmap]
rs9704047	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][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	nsv896896	chr11:4010409-4185595	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2758253	chr11:4055945-4510188	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	esv2759797	chr11:4055945-4510188	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv428248	chr11:4055945-4510188	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv832053	chr11:4096527-4330263	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2304891	RRM1	cis	cerebellum	SCAN
rs2304891	KRTAP5-4	cis	cerebellum	SCAN
rs2304891	POLR2L	cis	cerebellum	SCAN
rs2304891	OR52I2	cis	parietal	SCAN
rs2304891	TRIM21	cis	cerebellum	SCAN
rs2304891	OR51T1	cis	parietal	SCAN
rs2304891	ANO9	cis	parietal	SCAN
rs2304891	RRM1	cis	Artery Tibial	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4066200-4104200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:4066400-4107800	Weak transcription	Small Intestine	intestine
3	chr11:4070800-4108600	Weak transcription	HSMM	muscle
4	chr11:4079000-4112600	Weak transcription	Fetal Brain Female	brain
5	chr11:4081000-4104600	Weak transcription	Colonic Mucosa	Colon
6	chr11:4082600-4107400	Weak transcription	Stomach Mucosa	stomach
7	chr11:4086200-4115200	Weak transcription	NHDF-Ad	bronchial
8	chr11:4087600-4115000	Weak transcription	HSMMtube	muscle
9	chr11:4087800-4107800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:4088600-4107800	Weak transcription	Right Ventricle	heart
11	chr11:4091600-4107600	Weak transcription	Psoas Muscle	Psoas
12	chr11:4093600-4112600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr11:4093800-4103800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr11:4093800-4104000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr11:4093800-4115000	Weak transcription	Brain Germinal Matrix	brain
16	chr11:4093800-4115200	Weak transcription	Fetal Kidney	kidney
17	chr11:4094000-4103800	Weak transcription	Fetal Lung	lung
18	chr11:4094000-4106200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr11:4094000-4107800	Weak transcription	Brain Angular Gyrus	brain
20	chr11:4094000-4108600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr11:4094000-4108600	Weak transcription	Osteobl	bone
22	chr11:4094000-4115000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:4094000-4115000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr11:4094000-4115200	Weak transcription	Brain Substantia Nigra	brain
25	chr11:4095800-4109400	Weak transcription	K562	blood
26	chr11:4096000-4103800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:4096000-4103800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr11:4096000-4107600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr11:4096200-4104400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr11:4098200-4115000	Weak transcription	Hela-S3	cervix
31	chr11:4098400-4103800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr11:4099400-4107800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr11:4099400-4111200	Strong transcription	Fetal Thymus	thymus
34	chr11:4100200-4115200	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr11:4100400-4110400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr11:4100600-4106600	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr11:4100600-4115200	Weak transcription	NHLF	lung
38	chr11:4101000-4107400	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr11:4101000-4110600	Strong transcription	Primary B cells from peripheral blood	blood
40	chr11:4101400-4106200	Strong transcription	GM12878-XiMat	blood
41	chr11:4101400-4108000	Strong transcription	Primary T cells from cord blood	blood
42	chr11:4101400-4112800	Strong transcription	Thymus	Thymus
43	chr11:4101400-4113600	Strong transcription	Primary B cells from cord blood	blood
44	chr11:4101400-4114000	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr11:4101400-4114200	Strong transcription	Stomach Smooth Muscle	stomach
46	chr11:4101600-4106000	Strong transcription	HepG2	liver
47	chr11:4101600-4107000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr11:4101600-4113200	Strong transcription	Dnd41	blood
49	chr11:4101600-4113800	Strong transcription	Adipose Nuclei	Adipose
50	chr11:4101800-4104800	Strong transcription	Lung	lung

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