Variant report

Variant	rs10169925
Chromosome Location	chr2:113014605-113014606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPD	chr2:113014196-113014633	K562	blood:	n/a	n/a
2	GATA1	chr2:113014198-113014666	PBDE	blood:	n/a	n/a
3	TAL1	chr2:113014309-113014606	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113013051..113015199-chr2:113024386..113026807,2	K562	blood:
2	chr2:113010163..113016150-chr2:113027955..113035093,25	K562	blood:
3	chr2:113012601..113015047-chr2:113298969..113301494,2	K562	blood:
4	chr2:113009256..113015419-chr2:113031181..113035814,11	MCF-7	breast:
5	chr2:113012803..113017644-chr2:113018976..113023020,5	K562	blood:
6	chr2:113013310..113014991-chr2:113340459..113342175,2	MCF-7	breast:
7	chr2:113013729..113015547-chr2:113015611..113017197,2	K562	blood:

No data

Variant related genes	Relation type
ZC3H8	TF binding region
ENSG00000125630	Chromatin interaction
ENSG00000238951	Chromatin interaction
ENSG00000125611	Chromatin interaction
ENSG00000188177	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10864902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1343666	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2872046	0.95[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4848282	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6542047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6760417	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7591379	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[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	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv582703	chr2:112920219-113100014	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv874867	chr2:112930064-113038409	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	esv1805614	chr2:112949713-113048705	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10169925	POLR1B	cis	parietal	SCAN
rs10169925	SLC35F5	cis	cerebellum	SCAN
rs10169925	MERTK	cis	multi-tissue	Pritchard
rs10169925	CCDC138	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113012600-113016800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:113012600-113016800	Weak transcription	Fetal Heart	heart
3	chr2:113012600-113017200	Weak transcription	Stomach Mucosa	stomach
4	chr2:113012800-113017000	Weak transcription	Spleen	Spleen
5	chr2:113012800-113017200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:113013000-113015200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:113013000-113015600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr2:113013000-113016800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:113013000-113016800	Weak transcription	Fetal Kidney	kidney
10	chr2:113013000-113017000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:113013000-113017000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:113013000-113017000	Weak transcription	Brain Angular Gyrus	brain
13	chr2:113013000-113017000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr2:113013000-113017000	Weak transcription	Fetal Lung	lung
15	chr2:113013000-113017000	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:113013000-113017000	Weak transcription	Psoas Muscle	Psoas
17	chr2:113013000-113017000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:113013000-113017000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:113013000-113017000	Weak transcription	HMEC	breast
20	chr2:113013000-113017000	Weak transcription	NH-A	brain
21	chr2:113013000-113017000	Weak transcription	NHDF-Ad	bronchial
22	chr2:113013000-113017000	Weak transcription	NHEK	skin
23	chr2:113013000-113017000	Weak transcription	NHLF	lung
24	chr2:113013000-113017200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:113013000-113017200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:113013000-113017200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr2:113013000-113017200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr2:113013000-113017200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:113013000-113017200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:113013000-113017200	Weak transcription	Pancreas	Pancrea
31	chr2:113013000-113017400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:113013000-113018200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr2:113013000-113018200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr2:113013200-113015200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:113013200-113016200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:113013200-113016800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr2:113013200-113016800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:113013200-113016800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr2:113013200-113017000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:113013200-113017000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr2:113013200-113017000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr2:113013200-113017000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:113013200-113017000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:113013200-113017000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:113013200-113017000	Weak transcription	Liver	Liver
46	chr2:113013200-113017000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:113013200-113017000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:113013200-113017000	Weak transcription	Left Ventricle	heart
49	chr2:113013200-113017000	Weak transcription	Ovary	ovary
50	chr2:113013200-113017200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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