Variant report

Variant	rs10936352
Chromosome Location	chr3:100473505-100473506
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100468053..100471019-chr3:100472317..100474592,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1012364	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10936343	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10936345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10936346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[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];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1144112	0.81[EUR][1000 genomes]
rs1145335	0.81[EUR][1000 genomes]
rs1165261	0.81[EUR][1000 genomes]
rs1165536	0.80[EUR][1000 genomes]
rs12495397	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13059686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13092027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13098584	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1402252	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1829551	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs1903744	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36194934	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3773922	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41373752	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]
rs6441402	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6775161	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6775789	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6777763	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6781584	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6784601	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6793682	0.81[EUR][1000 genomes]
rs6806786	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6810101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7297	1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7612334	0.81[CEU][hapmap]
rs7614943	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7617184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7628413	0.88[CEU][hapmap];0.91[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7629279	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7634500	0.81[CEU][hapmap]
rs7642041	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs764684	0.85[CEU][hapmap]
rs7650690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7653531	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9811878	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9813835	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9815749	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9840505	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9849107	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876383	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
rs10936352	TFG	Cis_1M	lymphoblastoid	RTeQTL
rs10936352	ST3GAL6	cis	parietal	SCAN
rs10936352	TFG	cis	multi-tissue	Pritchard

Chromatin state (count:112 , 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	chr3:100432400-100474400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr3:100432800-100473600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:100434400-100478200	Weak transcription	Spleen	Spleen
5	chr3:100436000-100474400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:100437600-100475000	Strong transcription	Placenta	Placenta
7	chr3:100437800-100474400	Strong transcription	Duodenum Mucosa	Duodenum
8	chr3:100438800-100473800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:100441000-100474400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:100441000-100479400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:100444600-100474400	Strong transcription	HSMM	muscle
12	chr3:100445400-100473800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:100445400-100475600	Weak transcription	Pancreas	Pancrea
14	chr3:100447400-100473600	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr3:100447600-100474200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:100447600-100477200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:100448600-100474400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:100450000-100501000	Weak transcription	Esophagus	oesophagus
19	chr3:100453200-100479000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:100457200-100473600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:100457200-100474800	Strong transcription	NHDF-Ad	bronchial
22	chr3:100457200-100480200	Weak transcription	Brain Angular Gyrus	brain
23	chr3:100458000-100473600	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:100459200-100474600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:100459400-100478200	Weak transcription	Fetal Stomach	stomach
26	chr3:100463000-100474400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:100463000-100474400	Strong transcription	Adipose Nuclei	Adipose
28	chr3:100463400-100473600	Strong transcription	Fetal Muscle Trunk	muscle
29	chr3:100463600-100474800	Strong transcription	HSMMtube	muscle
30	chr3:100464200-100473600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:100465600-100478000	Weak transcription	Aorta	Aorta
32	chr3:100465600-100478000	Weak transcription	Fetal Heart	heart
33	chr3:100466800-100473800	Strong transcription	Fetal Intestine Large	intestine
34	chr3:100467000-100474400	Strong transcription	Primary T cells from cord blood	blood
35	chr3:100467400-100474400	Weak transcription	Fetal Brain Female	brain
36	chr3:100467400-100475800	Weak transcription	Thymus	Thymus
37	chr3:100467400-100497600	Weak transcription	Fetal Intestine Small	intestine
38	chr3:100467600-100473800	Weak transcription	Ovary	ovary
39	chr3:100467800-100474200	Weak transcription	Colonic Mucosa	Colon
40	chr3:100468200-100488600	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:100469000-100475800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:100469400-100480200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:100469600-100479200	Weak transcription	Fetal Brain Male	brain
44	chr3:100469800-100477600	Weak transcription	K562	blood
45	chr3:100469800-100498200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr3:100469800-100501400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr3:100470000-100474200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:100470200-100498400	Weak transcription	Right Ventricle	heart
49	chr3:100470600-100474600	Strong transcription	Left Ventricle	heart
50	chr3:100470800-100474000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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