Variant report

Variant	rs34949685
Chromosome Location	chr3:112271739-112271740
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	chr3:112270877..112274678-chr3:112278992..112281610,4	MCF-7	breast:
2	chr3:112270443..112273330-chr3:112277844..112281278,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138459	Chromatin interaction
ENSG00000144848	Chromatin interaction

Extended variants
information (count: 137 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10511317	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1072896	1.00[AFR][1000 genomes]
rs11919639	0.82[EUR][1000 genomes]
rs11921669	0.82[EUR][1000 genomes]
rs12630906	1.00[AFR][1000 genomes]
rs12634199	1.00[AFR][1000 genomes]
rs12637057	1.00[AFR][1000 genomes]
rs12637953	1.00[AFR][1000 genomes]
rs13059364	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13063173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13064534	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13065703	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13070342	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13071492	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13078401	1.00[AFR][1000 genomes]
rs13079599	1.00[AFR][1000 genomes]
rs13080547	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13080749	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13081201	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13081265	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13081632	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13086960	1.00[AFR][1000 genomes]
rs13088339	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13088349	1.00[EUR][1000 genomes]
rs13088467	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13094161	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13094649	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13095000	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13096943	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs16845067	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16845068	1.00[AFR][1000 genomes]
rs16845073	1.00[AFR][1000 genomes]
rs16859661	0.89[EUR][1000 genomes]
rs16859674	0.81[EUR][1000 genomes]
rs16859727	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16859758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16859775	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16859779	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859787	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16859793	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16859849	1.00[AFR][1000 genomes]
rs16859890	1.00[AFR][1000 genomes]
rs16859897	1.00[AFR][1000 genomes]
rs16859930	1.00[AFR][1000 genomes]
rs16859961	1.00[AFR][1000 genomes]
rs2220656	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2705526	0.85[EUR][1000 genomes]
rs28364588	1.00[AFR][1000 genomes]
rs28364589	1.00[AFR][1000 genomes]
rs28365853	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34080815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34139211	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34248586	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34284082	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34541731	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34596334	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34597203	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34645913	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34829517	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34889961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34962178	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35107041	0.82[EUR][1000 genomes]
rs35240469	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35255669	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35263368	1.00[AFR][1000 genomes]
rs35349986	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35512450	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35526995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35529363	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35692417	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35709173	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35725070	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35748518	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35803911	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35840933	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35931975	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36025914	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36031379	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36045008	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36061184	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36146261	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36153507	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3736269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3736270	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3736271	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3773698	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3773701	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3773704	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3773706	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3773710	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3821684	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55742760	1.00[EUR][1000 genomes]
rs56662636	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56856838	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56952692	1.00[AFR][1000 genomes]
rs56970524	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57224143	1.00[AFR][1000 genomes]
rs57346109	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58657519	1.00[AFR][1000 genomes]
rs58891772	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59191788	1.00[AFR][1000 genomes]
rs59279185	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59650289	1.00[AFR][1000 genomes]
rs59858117	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60112764	1.00[AFR][1000 genomes]
rs60321074	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60340975	1.00[AFR][1000 genomes]
rs60646325	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60733172	1.00[AFR][1000 genomes]
rs66486470	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66546764	1.00[AFR][1000 genomes]
rs66698345	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66791711	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66910014	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67021100	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs67204151	1.00[EUR][1000 genomes]
rs67513863	0.96[EUR][1000 genomes]
rs67940544	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67944354	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71317505	0.85[EUR][1000 genomes]
rs71317506	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71317507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71317508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71317510	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs724125	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73229350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73229353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73229398	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs958935	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs963541	1.00[AFR][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	nsv1003936	chr3:112125931-112274613	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv998309	chr3:112130290-112278804	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1006065	chr3:112147080-112276983	Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1005323	chr3:112171990-112274613	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv591301	chr3:112252532-112332629	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112234200-112272000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:112239600-112272200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:112244400-112274200	Weak transcription	Stomach Mucosa	stomach
4	chr3:112244400-112278200	Weak transcription	K562	blood
5	chr3:112244400-112278400	Weak transcription	HSMMtube	muscle
6	chr3:112245200-112273200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:112245800-112279600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:112247600-112279600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:112248400-112274200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:112249200-112275800	Weak transcription	Fetal Stomach	stomach
11	chr3:112249200-112276000	Weak transcription	Spleen	Spleen
12	chr3:112249200-112278200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:112249200-112278400	Weak transcription	Aorta	Aorta
14	chr3:112249200-112279600	Weak transcription	Esophagus	oesophagus
15	chr3:112249200-112279600	Weak transcription	Gastric	stomach
16	chr3:112249200-112279800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:112249400-112276200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:112249400-112279600	Weak transcription	Lung	lung
19	chr3:112251000-112274200	Weak transcription	Brain Angular Gyrus	brain
20	chr3:112252600-112278400	Weak transcription	Fetal Kidney	kidney
21	chr3:112253000-112273400	Weak transcription	Brain Substantia Nigra	brain
22	chr3:112253200-112278600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:112254200-112273600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:112257600-112274000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr3:112260000-112278200	Weak transcription	Fetal Brain Male	brain
26	chr3:112260400-112279600	Weak transcription	Pancreas	Pancrea
27	chr3:112265000-112276000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:112266000-112274200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr3:112266200-112278200	Weak transcription	Fetal Heart	heart
30	chr3:112266200-112278200	Weak transcription	NHLF	lung
31	chr3:112266200-112278400	Weak transcription	Colonic Mucosa	Colon
32	chr3:112266400-112278200	Weak transcription	NHEK	skin
33	chr3:112266800-112274400	Weak transcription	A549	lung
34	chr3:112266800-112278400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:112267000-112274000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:112267000-112274000	Weak transcription	HUVEC	blood vessel
37	chr3:112267000-112274600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:112267000-112278400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr3:112267000-112278400	Weak transcription	NHDF-Ad	bronchial
40	chr3:112267200-112274200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:112267200-112276000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:112267200-112276000	Weak transcription	Fetal Muscle Leg	muscle
43	chr3:112267200-112278400	Weak transcription	Thymus	Thymus
44	chr3:112267200-112279200	Weak transcription	Right Ventricle	heart
45	chr3:112267400-112274400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:112267600-112273000	Weak transcription	Brain Anterior Caudate	brain
47	chr3:112267600-112273000	Weak transcription	Brain Hippocampus Middle	brain
48	chr3:112267600-112274800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:112267600-112275800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr3:112267600-112278200	Weak transcription	Ovary	ovary

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