Variant report

Variant	rs2241885
Chromosome Location	chr15:78309553-78309554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1004855	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10519181	0.91[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs11072716	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11631578	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs11634607	0.86[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap]
rs11638311	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11852768	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12148365	0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap]
rs12591418	0.86[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap]
rs12594823	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs12901812	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12911332	0.89[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12916362	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1348257	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1442293	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1837913	0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap]
rs1992470	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2028546	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2044099	0.86[CHB][hapmap];0.97[CHD][hapmap];0.86[ASN][1000 genomes]
rs2867985	0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap]
rs3803380	0.86[CHB][hapmap];0.95[CHD][hapmap]
rs4395040	0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap]
rs4886553	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs4886554	0.86[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap]
rs4886994	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886996	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs4886999	0.86[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes]
rs4887000	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55704745	0.89[ASN][1000 genomes]
rs7166819	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7170746	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs7173128	0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7174489	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8030713	0.91[ASN][1000 genomes]
rs8030873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	esv1833316	chr15:78081307-78328108	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2241885	CLK3	cis	cerebellum	SCAN
rs2241885	HEXA	cis	parietal	SCAN
rs2241885	ISL2	cis	parietal	SCAN
rs2241885	CHRNA5	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78284600-78310200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr15:78285800-78309600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr15:78286000-78310400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr15:78287000-78316000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr15:78288400-78311000	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr15:78288600-78309600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr15:78288600-78309600	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr15:78288600-78309600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:78288600-78309600	Strong transcription	Thymus	Thymus
10	chr15:78288800-78309600	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr15:78288800-78310400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr15:78289000-78309800	Strong transcription	Primary T cells from cord blood	blood
13	chr15:78289400-78309800	Strong transcription	Dnd41	blood
14	chr15:78293600-78310000	Strong transcription	Primary hematopoietic stem cells	blood
15	chr15:78293800-78309600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr15:78296200-78316400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr15:78296200-78358200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr15:78297400-78310800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:78297600-78310400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr15:78298400-78309600	Genic enhancers	Liver	Liver
21	chr15:78300600-78316400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr15:78300800-78309600	Strong transcription	Fetal Stomach	stomach
23	chr15:78300800-78315400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr15:78301000-78310200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:78301000-78311400	Weak transcription	Right Atrium	heart
26	chr15:78301000-78316400	Weak transcription	Psoas Muscle	Psoas
27	chr15:78301200-78309600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:78301200-78309800	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr15:78301200-78315800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:78301400-78342200	Weak transcription	HMEC	breast
31	chr15:78301800-78313800	Strong transcription	Fetal Muscle Leg	muscle
32	chr15:78302200-78315400	Strong transcription	Fetal Muscle Trunk	muscle
33	chr15:78302400-78309800	Strong transcription	HSMMtube	muscle
34	chr15:78302800-78309600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:78302800-78309600	Strong transcription	NHLF	lung
36	chr15:78302800-78310400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:78303000-78310000	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr15:78303200-78309600	Strong transcription	Brain Angular Gyrus	brain
39	chr15:78303200-78309800	Strong transcription	Brain Cingulate Gyrus	brain
40	chr15:78303200-78309800	Strong transcription	Fetal Lung	lung
41	chr15:78303200-78342400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr15:78304000-78309800	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr15:78304400-78309800	Strong transcription	Osteobl	bone
44	chr15:78304600-78309800	Strong transcription	NH-A	brain
45	chr15:78304800-78309600	Strong transcription	GM12878-XiMat	blood
46	chr15:78304800-78310600	Strong transcription	NHDF-Ad	bronchial
47	chr15:78305000-78310200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr15:78305200-78310400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr15:78305400-78309600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr15:78305400-78311200	Weak transcription	K562	blood

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