Variant report

Variant	rs3796276
Chromosome Location	chr3:100465609-100465610
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	chr3:100461111..100462875-chr3:100463762..100466712,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114354	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1059363	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10755119	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs10936349	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11353	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1143774	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1143776	0.89[EUR][1000 genomes]
rs1143778	0.91[ASN][1000 genomes]
rs1143780	0.91[ASN][1000 genomes]
rs1143782	0.91[ASN][1000 genomes]
rs1144104	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1144105	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs1144106	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1144107	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1144108	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs1144109	0.91[ASN][1000 genomes]
rs1144110	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1144111	0.86[ASN][1000 genomes]
rs1144122	0.87[CEU][hapmap]
rs1144124	0.84[CEU][hapmap]
rs1144125	0.87[CEU][hapmap]
rs1144126	0.87[CEU][hapmap]
rs1145338	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs1145348	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs1165260	0.85[EUR][1000 genomes]
rs1165262	0.91[ASN][1000 genomes]
rs1165264	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs1165345	0.85[ASN][1000 genomes]
rs1165346	0.85[ASN][1000 genomes]
rs1165347	0.85[ASN][1000 genomes]
rs1165348	0.83[ASN][1000 genomes]
rs1165349	0.83[ASN][1000 genomes]
rs1165350	0.91[ASN][1000 genomes]
rs1165534	0.83[EUR][1000 genomes]
rs1165535	0.89[ASN][1000 genomes]
rs1185983	0.89[ASN][1000 genomes]
rs11921801	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs11921907	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs1384198	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1520652	0.80[EUR][1000 genomes]
rs1676343	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1676345	0.82[EUR][1000 genomes]
rs1676346	0.83[EUR][1000 genomes]
rs1676349	0.83[EUR][1000 genomes]
rs1676366	0.81[EUR][1000 genomes]
rs1680499	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1718272	0.83[CEU][hapmap]
rs1718275	0.87[CEU][hapmap]
rs1718279	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs1915309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2126540	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245857	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2447456	0.93[ASN][1000 genomes]
rs2449249	0.91[ASN][1000 genomes]
rs2449250	0.89[ASN][1000 genomes]
rs2460715	0.89[ASN][1000 genomes]
rs2460719	0.81[CEU][hapmap]
rs28364602	0.93[ASN][1000 genomes]
rs3087787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35685595	0.96[ASN][1000 genomes]
rs3821726	0.93[ASN][1000 genomes]
rs4088588	0.84[CEU][hapmap]
rs4144968	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs4367102	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4928070	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs4928081	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4928087	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs510303	0.91[ASN][1000 genomes]
rs586347	0.84[CEU][hapmap]
rs59010521	0.92[ASN][1000 genomes]
rs591728	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs605300	0.83[EUR][1000 genomes]
rs610854	0.84[CEU][hapmap]
rs6441383	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs6441384	0.83[CEU][hapmap]
rs648678	0.84[ASN][1000 genomes]
rs6767460	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs6770559	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs6773482	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6779489	0.85[CEU][hapmap]
rs6788891	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6789364	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs6798180	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs694612	0.81[CEU][hapmap]
rs7617579	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7627660	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7635652	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7637250	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7637272	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7644599	0.84[EUR][1000 genomes]
rs900235	0.81[CEU][hapmap]
rs9814836	0.91[ASN][1000 genomes]
rs9843956	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3796276	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	chr3:100437400-100472600	Strong transcription	Dnd41	blood
12	chr3:100437600-100475000	Strong transcription	Placenta	Placenta
13	chr3:100437800-100474400	Strong transcription	Duodenum Mucosa	Duodenum
14	chr3:100438800-100473800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:100441000-100470800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:100441000-100473000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:100441000-100474400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:100441000-100479400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:100443400-100472200	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr3:100443600-100466000	Strong transcription	Fetal Intestine Large	intestine
21	chr3:100444600-100471800	Strong transcription	Primary B cells from peripheral blood	blood
22	chr3:100444600-100474400	Strong transcription	HSMM	muscle
23	chr3:100445200-100470400	Strong transcription	HepG2	liver
24	chr3:100445400-100472200	Weak transcription	Psoas Muscle	Psoas
25	chr3:100445400-100473800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:100445400-100475600	Weak transcription	Pancreas	Pancrea
27	chr3:100446000-100470800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:100447200-100471400	Strong transcription	HMEC	breast
29	chr3:100447400-100473600	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr3:100447600-100474200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:100447600-100477200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:100448600-100474400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:100449600-100471000	Strong transcription	HUVEC	blood vessel
34	chr3:100449800-100472600	Strong transcription	Fetal Lung	lung
35	chr3:100450000-100472800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:100450000-100501000	Weak transcription	Esophagus	oesophagus
37	chr3:100450400-100472800	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr3:100451000-100468600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr3:100451400-100470000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr3:100452000-100471200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:100453200-100472000	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr3:100453200-100479000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr3:100453400-100471400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:100453600-100473000	Weak transcription	Stomach Mucosa	stomach
45	chr3:100453800-100468600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:100454000-100471800	Strong transcription	NH-A	brain
47	chr3:100454200-100472600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:100455200-100471200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr3:100456200-100470200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:100456800-100471000	Strong transcription	HUES64 Cell Line	embryonic stem cell

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