Variant report

Variant	rs2494643
Chromosome Location	chr10:90846938-90846939
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:90835486..90838923-chr10:90846625..90848584,3	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10509563	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202955	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12268223	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1937333	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1937336	0.84[CEU][hapmap]
rs2000360	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247755	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs2252139	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2253515	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2255465	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2489882	0.81[AMR][1000 genomes]
rs2801533	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2801536	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2801539	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841016	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841019	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2841021	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841024	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2841025	0.81[ASN][1000 genomes]
rs2841026	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841030	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2841032	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34582012	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4471339	0.85[ASN][1000 genomes]
rs7076595	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7081499	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7084166	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100350	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7914848	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7915156	0.80[YRI][hapmap]
rs7919067	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9421696	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9633743	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9651494	1.00[CEU][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv831943	chr10:90664836-90865834	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv467416	chr10:90815975-90889997	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv551842	chr10:90815975-90889997	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
6	nsv895880	chr10:90816060-90874029	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv831944	chr10:90822654-90967018	Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
8	nsv467418	chr10:90826252-90874468	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv551843	chr10:90826252-90874468	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv2829934	chr10:90826779-90874468	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv2758235	chr10:90835064-91017486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv2759775	chr10:90835064-91017486	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv895881	chr10:90842431-90940003	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2494643	IFIT5	cis	cerebellum	SCAN
rs2494643	KIF11	cis	parietal	SCAN
rs2494643	HECTD2	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90841800-90861000	Weak transcription	Aorta	Aorta
2	chr10:90842000-90851600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr10:90843800-90847400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr10:90844200-90850400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr10:90844400-90847400	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr10:90844600-90847200	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr10:90845200-90850600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr10:90845200-90855000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr10:90845400-90847000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr10:90845400-90850000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr10:90845400-90850600	Weak transcription	Brain Substantia Nigra	brain
12	chr10:90845600-90847000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr10:90845800-90847200	Enhancers	H9 Cell Line	embryonic stem cell
14	chr10:90845800-90847400	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr10:90845800-90847400	Flanking Active TSS	Dnd41	blood
16	chr10:90846000-90847000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr10:90846000-90847200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr10:90846000-90847400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr10:90846000-90847400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr10:90846200-90847000	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr10:90846200-90847200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr10:90846200-90847200	Flanking Active TSS	NHDF-Ad	bronchial
23	chr10:90846200-90847400	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr10:90846200-90847400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr10:90846200-90847400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr10:90846200-90847400	Flanking Active TSS	HSMMtube	muscle
27	chr10:90846400-90847000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr10:90846400-90847200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr10:90846400-90847200	Enhancers	Fetal Muscle Leg	muscle
30	chr10:90846400-90847200	Flanking Active TSS	NHLF	lung
31	chr10:90846400-90847400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr10:90846400-90847400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr10:90846400-90847400	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr10:90846400-90847400	Flanking Active TSS	Osteobl	bone
35	chr10:90846600-90847000	Enhancers	H1 Cell Line	embryonic stem cell
36	chr10:90846600-90847000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr10:90846600-90847000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr10:90846600-90847000	Weak transcription	Brain Angular Gyrus	brain
39	chr10:90846600-90847000	Enhancers	Placenta	Placenta
40	chr10:90846600-90847000	Flanking Active TSS	Psoas Muscle	Psoas
41	chr10:90846600-90847000	Flanking Active TSS	K562	blood
42	chr10:90846600-90847200	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr10:90846600-90847200	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr10:90846600-90847200	Active TSS	Duodenum Mucosa	Duodenum
45	chr10:90846600-90847200	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr10:90846600-90847200	Active TSS	Stomach Smooth Muscle	stomach
47	chr10:90846600-90847200	Enhancers	GM12878-XiMat	blood
48	chr10:90846600-90847200	Flanking Active TSS	HSMM	muscle
49	chr10:90846600-90847400	Enhancers	Colon Smooth Muscle	Colon
50	chr10:90846800-90847200	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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