Variant report

Variant	rs10900229
Chromosome Location	chr10:46121046-46121047
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	MAFK	chr10:46120857-46121058	HepG2	liver:	n/a	chr10:46120958-46120974 chr10:46120957-46120971 chr10:46120963-46120972

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:46119155..46121505-chr10:46123417..46125347,2	K562	blood:
2	chr10:46114504..46116617-chr10:46119819..46121528,2	K562	blood:

Variant related genes	Relation type
ZFAND4	TF binding region
ENSG00000172671	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10466245	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10900221	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10900223	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10900224	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10900230	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900232	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900233	0.80[EUR][1000 genomes]
rs10900235	0.82[EUR][1000 genomes]
rs11239528	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs11239536	0.87[ASN][1000 genomes]
rs11239538	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239545	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11239549	0.83[EUR][1000 genomes]
rs11239551	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11239569	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239571	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239582	0.90[LWK][hapmap];0.82[AFR][1000 genomes]
rs12242611	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12243153	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12243845	0.81[LWK][hapmap]
rs12246131	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12249012	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12257537	0.89[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[LWK][hapmap];0.89[ASN][1000 genomes]
rs12257549	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12267385	0.90[LWK][hapmap];0.82[AFR][1000 genomes]
rs12269403	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2291428	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2291429	0.87[ASN][1000 genomes]
rs3802548	0.83[ASN][1000 genomes]
rs55665473	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58865519	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59390133	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61854096	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61854123	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61854156	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7076198	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7086046	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72796498	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs970548	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv895112	chr10:46012620-46202216	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1050880	chr10:46091441-46160597	Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv540588	chr10:46091441-46160597	ZNF genes & repeats Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv947911	chr10:46116371-46136816	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10900229	ALOX5	cis	parietal	SCAN
rs10900229	ZNF32	cis	parietal	SCAN
rs10900229	FAM21A///FAM21B	N/A	lymphoblastoid	RTeQTL
rs10900229	ALOX5	Cis_1M	lymphoblastoid	RTeQTL
rs10900229	ZNF485	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:46090600-46167600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:46096200-46142000	Weak transcription	Brain Anterior Caudate	brain
3	chr10:46096400-46121600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr10:46096400-46121800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr10:46097800-46121600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr10:46097800-46121800	Weak transcription	Psoas Muscle	Psoas
7	chr10:46098200-46153400	Weak transcription	HSMM	muscle
8	chr10:46099200-46122200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr10:46100200-46142600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr10:46101600-46121800	Weak transcription	Brain Substantia Nigra	brain
11	chr10:46103000-46121800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr10:46103000-46121800	Weak transcription	Spleen	Spleen
13	chr10:46103400-46130600	Weak transcription	Fetal Brain Male	brain
14	chr10:46103400-46142200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr10:46103600-46121800	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr10:46103600-46132600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr10:46103800-46121400	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr10:46103800-46134600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr10:46104400-46151400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr10:46104800-46121400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr10:46105000-46121800	Weak transcription	Pancreas	Pancrea
22	chr10:46105600-46141600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr10:46105800-46123800	Weak transcription	NHEK	skin
24	chr10:46106400-46121600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr10:46106400-46137000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr10:46106400-46141400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr10:46106400-46142000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr10:46106800-46128000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr10:46106800-46142000	Weak transcription	Fetal Kidney	kidney
30	chr10:46106800-46146400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr10:46107000-46125600	Weak transcription	Fetal Brain Female	brain
32	chr10:46107800-46121800	Weak transcription	Gastric	stomach
33	chr10:46107800-46141800	Weak transcription	Colon Smooth Muscle	Colon
34	chr10:46107800-46142000	Weak transcription	Esophagus	oesophagus
35	chr10:46108000-46121600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr10:46108000-46121800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr10:46108000-46155800	Weak transcription	Brain Angular Gyrus	brain
38	chr10:46108200-46142000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr10:46108400-46121400	Weak transcription	Thymus	Thymus
40	chr10:46108400-46121800	Weak transcription	Left Ventricle	heart
41	chr10:46108400-46121800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr10:46108400-46121800	Weak transcription	Right Ventricle	heart
43	chr10:46108400-46122000	Weak transcription	Ovary	ovary
44	chr10:46108400-46122800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr10:46108400-46123000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr10:46108400-46142000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr10:46108400-46149400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr10:46108400-46167000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr10:46108600-46121400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr10:46108600-46121400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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