Variant report

Variant	rs2291429
Chromosome Location	chr10:45958881-45958882
allele	A/C/G
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	POLR2A	chr10:45958529-45959118	HL-60	blood:	n/a	n/a
2	POLR2A	chr10:45958343-45959008	GM12892	blood:	n/a	n/a
3	POLR2A	chr10:45958680-45958977	GM12878	blood:	n/a	n/a
4	POLR2A	chr10:45958317-45959987	GM12878	blood:	n/a	n/a
5	POLR2A	chr10:45958356-45958998	GM12878	blood:	n/a	n/a
6	HMGN3	chr10:45958732-45959009	K562	blood:	n/a	n/a

Variant related genes	Relation type
MARCH8	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10466245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10793620	0.84[CEU][hapmap]
rs10900220	0.85[CEU][hapmap]
rs10900221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10900222	0.84[CEU][hapmap]
rs10900223	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10900224	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10900229	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs10900230	0.87[ASN][1000 genomes]
rs10900232	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11239528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239532	1.00[YRI][hapmap]
rs11239535	0.89[CEU][hapmap]
rs11239536	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239538	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239541	0.81[CEU][hapmap]
rs11239545	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239548	0.84[CEU][hapmap]
rs11239549	0.93[EUR][1000 genomes]
rs11239550	0.84[CEU][hapmap]
rs11239551	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11239569	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12242611	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12243153	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12246131	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12249012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12257537	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12257549	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12269403	0.90[ASN][1000 genomes]
rs2291428	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2310783	1.00[YRI][hapmap]
rs3802548	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55665473	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58865519	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59390133	0.87[ASN][1000 genomes]
rs61854096	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61854123	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61854156	0.87[ASN][1000 genomes]
rs7076198	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7086046	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72796498	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs970548	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[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	nsv430166	chr10:45668894-46148794	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv993428	chr10:45742877-46224333	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv895108	chr10:45878908-46224333	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
4	nsv895109	chr10:45882741-46210665	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv1043536	chr10:45915941-46076235	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Blood metabolite levels	24816252	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2291429	FAM21A///FAM21B	N/A	lymphoblastoid	RTeQTL
rs2291429	ALOX5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45938600-45967200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:45938600-45967200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr10:45943200-45965400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr10:45948000-45963600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr10:45948600-45959800	Strong transcription	Fetal Intestine Small	intestine
6	chr10:45948600-45959800	Strong transcription	Fetal Stomach	stomach
7	chr10:45949200-45965600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr10:45949400-45959800	Strong transcription	Primary T cells from cord blood	blood
9	chr10:45950000-45967200	Weak transcription	Psoas Muscle	Psoas
10	chr10:45950200-45959400	Strong transcription	Fetal Intestine Large	intestine
11	chr10:45950200-45960600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr10:45950400-45959400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr10:45950400-45959600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr10:45950400-45966200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr10:45950800-45965600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr10:45951000-45960600	Weak transcription	Fetal Brain Male	brain
17	chr10:45951000-45965600	Weak transcription	Brain Germinal Matrix	brain
18	chr10:45951200-45959000	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr10:45951200-45959400	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr10:45951200-45959600	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr10:45951200-45959600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr10:45951200-45960600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr10:45951400-45962200	Weak transcription	HMEC	breast
24	chr10:45951600-45959400	Strong transcription	Ovary	ovary
25	chr10:45951600-45959800	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr10:45951600-45965600	Weak transcription	Small Intestine	intestine
27	chr10:45952000-45959400	Strong transcription	Fetal Muscle Trunk	muscle
28	chr10:45953000-45959000	Strong transcription	Rectal Smooth Muscle	rectum
29	chr10:45953000-45965600	Weak transcription	Colon Smooth Muscle	Colon
30	chr10:45953600-45969200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr10:45954600-45959200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr10:45954600-45965600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr10:45954800-45960200	Weak transcription	Brain Hippocampus Middle	brain
34	chr10:45955000-45965600	Weak transcription	NHLF	lung
35	chr10:45955200-45960200	Weak transcription	Gastric	stomach
36	chr10:45955600-45959000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr10:45955600-45960600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr10:45955600-45962400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr10:45955600-45965400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr10:45955800-45959000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr10:45955800-45959600	Weak transcription	Right Ventricle	heart
42	chr10:45956000-45960600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr10:45956200-45960600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr10:45956200-45965400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr10:45956400-45966800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr10:45956600-45960600	Weak transcription	Brain Angular Gyrus	brain
47	chr10:45956600-45965600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr10:45956800-45960200	Weak transcription	K562	blood
49	chr10:45956800-45960600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr10:45956800-45960600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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