Variant report

Variant	rs41373752
Chromosome Location	chr3:100458996-100458997
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	POLR2A	chr3:100458691-100460151	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:100458697-100459450	K562	blood:	n/a	n/a
3	POLR2A	chr3:100458914-100459024	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100456375..100459154-chr3:100461362..100464056,3	K562	blood:

Variant related genes	Relation type
TFG	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1012364	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936343	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936352	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10936355	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1144112	0.83[EUR][1000 genomes]
rs1145335	0.83[EUR][1000 genomes]
rs1165261	0.82[EUR][1000 genomes]
rs1165536	0.82[EUR][1000 genomes]
rs12495397	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13059686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13092027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13098584	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1402252	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1829551	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs1903744	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36194934	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3773922	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441402	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6775161	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6775789	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6777763	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6781584	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6784601	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6793682	0.82[EUR][1000 genomes]
rs6806786	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6810101	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7297	1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7612334	0.81[CEU][hapmap]
rs7614943	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7617184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628413	0.88[CEU][hapmap];0.91[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7629279	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7634500	0.81[CEU][hapmap]
rs7642041	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs764684	0.85[CEU][hapmap]
rs7650690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7653531	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9811878	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9813835	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9815749	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9840505	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9849107	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9876383	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751965	chr3:100299310-100462527	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	esv2751966	chr3:100299310-100468500	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS 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	17 gene(s)	inside rSNPs	diseases
3	esv2751968	chr3:100299329-100476713	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv432466	chr3:100299329-100476713	Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv2751969	chr3:100312499-100479384	Strong transcription Weak transcription Enhancers Active TSS Flanking 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 miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv877220	chr3:100324442-100467018	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv2751971	chr3:100342493-100468500	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv2751972	chr3:100342493-100493062	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
9	nsv432469	chr3:100342493-100493062	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
10	nsv460787	chr3:100350745-100467018	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv591164	chr3:100350745-100467018	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	esv2751973	chr3:100354170-100476713	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription 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 miRNA target site	17 gene(s)	inside rSNPs	diseases
13	esv2751974	chr3:100354170-100476713	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs41373752	ST3GAL6	cis	parietal	SCAN
rs41373752	TFG	Cis_1M	lymphoblastoid	RTeQTL
rs41373752	TFG	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100429800-100475000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:100430400-100473000	Strong transcription	Fetal Thymus	thymus
3	chr3:100431200-100473000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:100432400-100474400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr3:100432800-100473600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:100433000-100472400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr3:100434400-100478200	Weak transcription	Spleen	Spleen
8	chr3:100436000-100474400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:100436600-100471600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:100436800-100473000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:100437000-100461600	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr3:100437400-100472600	Strong transcription	Dnd41	blood
13	chr3:100437600-100475000	Strong transcription	Placenta	Placenta
14	chr3:100437800-100474400	Strong transcription	Duodenum Mucosa	Duodenum
15	chr3:100438800-100473800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:100441000-100470800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:100441000-100473000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:100441000-100474400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:100441000-100479400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:100443200-100462200	Strong transcription	Adipose Nuclei	Adipose
21	chr3:100443400-100472200	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr3:100443600-100466000	Strong transcription	Fetal Intestine Large	intestine
23	chr3:100444600-100471800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr3:100444600-100474400	Strong transcription	HSMM	muscle
25	chr3:100445200-100470400	Strong transcription	HepG2	liver
26	chr3:100445400-100472200	Weak transcription	Psoas Muscle	Psoas
27	chr3:100445400-100473800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:100445400-100475600	Weak transcription	Pancreas	Pancrea
29	chr3:100445800-100459000	Weak transcription	Fetal Brain Male	brain
30	chr3:100446000-100470800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:100447200-100471400	Strong transcription	HMEC	breast
32	chr3:100447400-100460000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr3:100447400-100473600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr3:100447600-100461800	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr3:100447600-100474200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:100447600-100477200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:100448600-100474400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:100449000-100460600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:100449000-100461600	Strong transcription	Primary B cells from cord blood	blood
40	chr3:100449600-100459200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:100449600-100471000	Strong transcription	HUVEC	blood vessel
42	chr3:100449800-100461600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:100449800-100462200	Strong transcription	GM12878-XiMat	blood
44	chr3:100449800-100472600	Strong transcription	Fetal Lung	lung
45	chr3:100450000-100472800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:100450000-100501000	Weak transcription	Esophagus	oesophagus
47	chr3:100450200-100460400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:100450400-100472800	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr3:100451000-100468600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr3:100451400-100470000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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