Variant report

Variant	rs2797493
Chromosome Location	chr10:5794025-5794026
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:5781966..5784201-chr10:5791463..5794331,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10737018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10905029	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10905066	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11596702	0.81[MEX][hapmap]
rs1418739	0.87[ASW][hapmap];1.00[YRI][hapmap]
rs2254067	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2380209	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2386620	0.81[MEX][hapmap]
rs2669135	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2669137	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2669138	0.84[AFR][1000 genomes]
rs2797484	0.97[ASN][1000 genomes]
rs2797486	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2797487	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2797491	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2797494	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2797501	0.87[ASW][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[ASN][1000 genomes]
rs4423100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56352451	0.94[ASN][1000 genomes]
rs61016063	0.91[EUR][1000 genomes]
rs7082754	1.00[YRI][hapmap]
rs7900361	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs7907687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9423934	0.87[ASW][hapmap];1.00[YRI][hapmap]

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	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	esv2759729	chr10:5557024-5804780	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	esv2758209	chr10:5637111-5804780	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer 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 miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2797493	CALML5	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5762200-5795400	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr10:5762400-5794600	Strong transcription	Primary T helper cells PMA-I stimulated	--
3	chr10:5762600-5843400	Strong transcription	Dnd41	blood
4	chr10:5762800-5843000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr10:5763000-5795000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr10:5768000-5849400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr10:5775200-5794400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr10:5777000-5795800	Strong transcription	Fetal Thymus	thymus
9	chr10:5779000-5804600	Strong transcription	A549	lung
10	chr10:5779200-5796600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr10:5779400-5795200	Strong transcription	Primary B cells from cord blood	blood
12	chr10:5781400-5818600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr10:5781600-5794400	Strong transcription	Adipose Nuclei	Adipose
14	chr10:5781600-5796200	Strong transcription	Fetal Muscle Leg	muscle
15	chr10:5781600-5796400	Strong transcription	Placenta	Placenta
16	chr10:5783400-5796600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr10:5783400-5816600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr10:5784800-5799400	Weak transcription	Colon Smooth Muscle	Colon
19	chr10:5784800-5818000	Weak transcription	Stomach Mucosa	stomach
20	chr10:5785800-5796800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr10:5786200-5816400	Weak transcription	Right Atrium	heart
22	chr10:5788000-5795000	Strong transcription	GM12878-XiMat	blood
23	chr10:5788000-5818000	Strong transcription	Duodenum Mucosa	Duodenum
24	chr10:5789200-5795600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr10:5789200-5795800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr10:5789200-5798600	Weak transcription	Brain Angular Gyrus	brain
27	chr10:5789200-5799000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr10:5789200-5804400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr10:5789400-5798600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr10:5790200-5795800	Strong transcription	Primary T cells from cord blood	blood
31	chr10:5790400-5798800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr10:5790600-5794200	Weak transcription	Brain Anterior Caudate	brain
33	chr10:5790600-5794200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr10:5790600-5798400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr10:5790600-5800200	Weak transcription	Fetal Brain Male	brain
36	chr10:5790800-5798600	Weak transcription	Brain Substantia Nigra	brain
37	chr10:5790800-5799000	Weak transcription	HSMMtube	muscle
38	chr10:5790800-5799200	Weak transcription	HUVEC	blood vessel
39	chr10:5791000-5798600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr10:5791200-5798000	Weak transcription	HMEC	breast
41	chr10:5791200-5799200	Weak transcription	Small Intestine	intestine
42	chr10:5791400-5798400	Weak transcription	Colonic Mucosa	Colon
43	chr10:5791400-5798600	Weak transcription	Fetal Kidney	kidney
44	chr10:5791400-5798600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr10:5791400-5798800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr10:5791600-5794200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr10:5791600-5794200	Weak transcription	Spleen	Spleen
48	chr10:5791600-5794600	Weak transcription	Aorta	Aorta
49	chr10:5791600-5798400	Weak transcription	Psoas Muscle	Psoas
50	chr10:5791600-5798600	Weak transcription	Brain Germinal Matrix	brain

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