Variant report

Variant	rs13100173
Chromosome Location	chr3:50332697-50332698
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:50332450-50332777	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:50331738-50333675	K562	blood:	n/a	n/a
3	POLR2A	chr3:50331951-50333745	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:50332581-50333803	K562	blood:	n/a	n/a
5	POLR2A	chr3:50331371-50332978	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50296030..50318456-chr3:50318822..50339499,66	MCF-7	breast:
2	chr3:50242260..50244177-chr3:50332568..50334684,2	K562	blood:
3	chr3:50327926..50342388-chr3:50350886..50359960,36	MCF-7	breast:
4	chr3:50324564..50342616-chr3:50350801..50362499,49	MCF-7	breast:
5	chr3:50327690..50333528-chr3:50363706..50369146,7	MCF-7	breast:

No data

Variant related genes	Relation type
IFRD2	TF binding region
ENSG00000068001	Chromatin interaction
ENSG00000188338	Chromatin interaction
ENSG00000232352	Chromatin interaction
ENSG00000012171	Chromatin interaction
ENSG00000179564	Chromatin interaction
ENSG00000230454	Chromatin interaction
ENSG00000114383	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2236947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34136796	0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv590250	chr3:50153356-50332697	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
6	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
7	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
8	nsv590251	chr3:50158774-50337422	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
10	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
11	nsv523560	chr3:50172397-50339163	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
12	nsv1014256	chr3:50187646-50339163	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
13	nsv536565	chr3:50187646-50339163	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
14	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
15	nsv590253	chr3:50196418-50337422	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
16	esv2757870	chr3:50198478-50371377	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
17	esv2759148	chr3:50198478-50371377	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
18	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
19	nsv590254	chr3:50243510-50388607	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
20	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
21	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
22	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
23	nsv590257	chr3:50302830-50393640	Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
24	nsv590256	chr3:50302830-50420554	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
25	nsv876774	chr3:50302830-50436827	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
26	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
27	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
28	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs13100173	RNF123	cis	parietal	SCAN
rs13100173	RBM6	cis	cerebellum	SCAN
rs13100173	GNL3	cis	parietal	SCAN
rs13100173	HYAL3	cis	Artery Aorta	GTEx
rs13100173	HYAL3	cis	Esophagus Mucosa	GTEx
rs13100173	HYAL3	cis	Whole Blood	GTEx
rs13100173	CCDC71	cis	parietal	SCAN
rs13100173	NISCH	cis	cerebellum	SCAN
rs13100173	HYAL3	cis	Thyroid	GTEx
rs13100173	HYAL3	cis	Temporal Cortex	GTEx
rs13100173	NME6	cis	cerebellum	SCAN
rs13100173	HYAL3	cis	Heart Left Ventricle	GTEx
rs13100173	HYAL3	cis	Frontal Cortex	GTEx
rs13100173	HYAL3	cis	Esophagus Muscularis	GTEx
rs13100173	STAT3	trans	lymphoblastoid	seeQTL
rs13100173	HYAL3	cis	multi-tissue	Pritchard
rs13100173	ARIH2	cis	cerebellum	SCAN
rs13100173	CCDC51	cis	cerebellum	SCAN
rs13100173	PTH1R	cis	parietal	SCAN
rs13100173	HYAL3,NAT6	cis	brain	BrainEAC
rs13100173	HYAL3	cis	cerebellum	SCAN
rs13100173	HYAL3	cis	lung	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50330200-50334600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:50330400-50334200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:50330400-50335600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:50330400-50335600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:50330400-50335600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:50330400-50335600	Weak transcription	Fetal Lung	lung
7	chr3:50330400-50335800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:50330400-50336000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:50330600-50333400	Weak transcription	Brain Germinal Matrix	brain
10	chr3:50330600-50333600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:50330600-50333600	Weak transcription	NHEK	skin
12	chr3:50330600-50333800	Weak transcription	Fetal Brain Female	brain
13	chr3:50330600-50334200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:50330600-50334400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:50330600-50334400	Weak transcription	Placenta	Placenta
16	chr3:50330600-50334400	Weak transcription	NHLF	lung
17	chr3:50330600-50334600	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr3:50330600-50334600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:50330600-50335000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:50330600-50335000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr3:50330600-50335200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr3:50330600-50335400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:50330600-50335400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr3:50330600-50335400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:50330600-50335600	Weak transcription	Primary B cells from cord blood	blood
26	chr3:50330600-50335600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:50330600-50335600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr3:50330600-50335600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr3:50330600-50335600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:50330600-50335600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:50330600-50335600	Weak transcription	Thymus	Thymus
32	chr3:50330600-50335600	Weak transcription	HSMM	muscle
33	chr3:50330600-50335600	Weak transcription	HUVEC	blood vessel
34	chr3:50330600-50335600	Weak transcription	Osteobl	bone
35	chr3:50330600-50335800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr3:50330600-50335800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr3:50330600-50335800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr3:50330600-50335800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:50330600-50335800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr3:50330600-50335800	Weak transcription	Primary T cells from cord blood	blood
41	chr3:50330600-50335800	Weak transcription	Ovary	ovary
42	chr3:50330600-50335800	Weak transcription	Right Atrium	heart
43	chr3:50330600-50335800	Weak transcription	A549	lung
44	chr3:50330600-50335800	Weak transcription	NHDF-Ad	bronchial
45	chr3:50330800-50333000	Weak transcription	Fetal Stomach	stomach
46	chr3:50330800-50333200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:50330800-50333200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:50330800-50333200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:50330800-50333400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:50330800-50333400	Weak transcription	Fetal Intestine Small	intestine

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