Variant report

Variant	rs4445550
Chromosome Location	chr10:5009347-5009348
allele	A/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	JUND	chr10:5009035-5009849	A549	lung:	n/a	n/a
2	HEY1	chr10:5009315-5012006	HepG2	liver:	n/a	n/a
3	BCL3	chr10:5008350-5009779	A549	lung:	n/a	chr10:5008426-5008435
4	POLR2A	chr10:5009148-5009578	HepG2	liver:	n/a	n/a
5	POLR2A	chr10:5008947-5009777	HepG2	liver:	n/a	n/a
6	POLR2A	chr10:5005321-5012094	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:5003815..5006768-chr10:5008724..5010986,2	K562	blood:
2	chr10:5005241..5007443-chr10:5009347..5011794,2	MCF-7	breast:
3	chr10:5008134..5010940-chr10:5050778..5053121,2	K562	blood:

Variant related genes	Relation type
ENSG00000238840	TF binding region
ENSG00000187134	Chromatin interaction
ENSG00000238840	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11252853	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11252861	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12263706	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12264439	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12264914	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12774134	1.00[JPT][hapmap]
rs1937859	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3890593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3890643	0.83[AMR][1000 genomes]
rs3898029	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3923936	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3925947	0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4332428	1.00[JPT][hapmap]
rs4344395	1.00[JPT][hapmap]
rs4397735	1.00[JPT][hapmap]
rs4512733	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6601882	0.89[YRI][hapmap]
rs6601884	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6650153	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7068923	1.00[JPT][hapmap]
rs7074155	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7076886	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7083234	0.89[YRI][hapmap]
rs7089378	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72769971	0.84[ASN][1000 genomes]
rs7893456	0.84[ASN][1000 genomes]
rs7906245	0.82[AMR][1000 genomes]
rs7908994	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7909151	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7915365	1.00[JPT][hapmap]
rs7916500	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs7916644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894792	chr10:4832920-5498724	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv948794	chr10:4863093-5227382	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1045155	chr10:4872239-5211318	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040343	chr10:4872814-5196815	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540462	chr10:4872814-5196815	Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv869470	chr10:4878904-5203685	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv466713	chr10:4901798-5319679	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv549881	chr10:4901798-5319679	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	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
10	nsv1050246	chr10:4927428-5211318	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv549882	chr10:4943518-5203864	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv2763913	chr10:4961021-5321407	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv894794	chr10:4972761-5121745	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription 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	14 gene(s)	inside rSNPs	diseases
14	nsv430122	chr10:4986040-5134511	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv825221	chr10:4999349-5046239	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
16	nsv947726	chr10:5008069-5012084	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	nsv1039386	chr10:5008383-5348491	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4445550	AKR1C1	cis	Whole Blood	GTEx
rs4445550	ATP5C1	cis	parietal	SCAN
rs4445550	AKR1C2	cis	parietal	SCAN
rs4445550	AKR1C2	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:4998200-5023800	Weak transcription	Gastric	stomach
2	chr10:5004800-5023800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr10:5005600-5009600	Active TSS	Right Atrium	heart
4	chr10:5005800-5011000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr10:5005800-5027400	Weak transcription	Fetal Stomach	stomach
6	chr10:5005800-5045800	Weak transcription	HSMMtube	muscle
7	chr10:5006000-5023800	Weak transcription	Esophagus	oesophagus
8	chr10:5006000-5023800	Weak transcription	Left Ventricle	heart
9	chr10:5006000-5024000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr10:5006200-5011000	Weak transcription	Ovary	ovary
11	chr10:5006200-5011200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr10:5006800-5010800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr10:5006800-5011200	Weak transcription	Osteobl	bone
14	chr10:5007200-5009400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr10:5007200-5010600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr10:5007200-5011200	Weak transcription	Aorta	Aorta
17	chr10:5007200-5011600	Weak transcription	Fetal Heart	heart
18	chr10:5007200-5021600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr10:5007200-5023200	Weak transcription	Fetal Intestine Large	intestine
20	chr10:5007200-5023600	Weak transcription	Fetal Intestine Small	intestine
21	chr10:5007200-5023800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr10:5007400-5010800	Weak transcription	Fetal Brain Female	brain
23	chr10:5007400-5011000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr10:5007400-5023800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr10:5007400-5023800	Weak transcription	Right Ventricle	heart
26	chr10:5007400-5024200	Weak transcription	NHEK	skin
27	chr10:5007600-5010800	Weak transcription	Brain Germinal Matrix	brain
28	chr10:5008000-5009600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr10:5008000-5009600	Transcr. at gene 5' and 3'	A549	lung
30	chr10:5008000-5010800	Weak transcription	Psoas Muscle	Psoas
31	chr10:5008000-5011000	Weak transcription	K562	blood
32	chr10:5008200-5021000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr10:5008200-5044000	Weak transcription	Fetal Brain Male	brain
34	chr10:5008400-5010800	Weak transcription	NHDF-Ad	bronchial
35	chr10:5008600-5009600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr10:5008800-5015800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr10:5008800-5023200	Weak transcription	Stomach Mucosa	stomach
38	chr10:5009200-5009600	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
39	chr10:5009200-5009600	Transcr. at gene 5' and 3'	Liver	Liver
40	chr10:5009200-5009600	Flanking Active TSS	HepG2	liver

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