Variant report

Variant	rs34541731
Chromosome Location	chr3:112324054-112324055
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr3:112323169-112324617	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr3:112324032-112324576	H1-neurons	neurons:	n/a	n/a
3	TCF12	chr3:112323163-112324732	SK-N-SH	brain:	n/a	n/a
4	REST	chr3:112323980-112324668	H1-neurons	neurons:	n/a	n/a
5	MXI1	chr3:112323893-112325036	IMR90	lung:	n/a	n/a
6	FOS	chr3:112323248-112324640	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr3:112323979-112324668	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr3:112323995-112324390	SK-N-SH	brain:	n/a	n/a
9	MAX	chr3:112323997-112324517	SK-N-SH	brain:	n/a	n/a
10	GATA3	chr3:112323258-112324540	SK-N-SH	brain:	n/a	n/a
11	GATA3	chr3:112323174-112324796	SK-N-SH	brain:	n/a	chr3:112324784-112324795
12	REST	chr3:112323841-112324808	H1-neurons	neurons:	n/a	n/a
13	POLR2A	chr3:112324022-112324603	U87	brain:	n/a	n/a
14	POLR2A	chr3:112324022-112324608	U87	brain:	n/a	n/a
15	JUN	chr3:112323285-112324669	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr3:112324024-112324705	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr3:112323386-112324592	IMR90	lung:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112321970..112325392-chr3:112326276..112329430,4	K562	blood:
2	chr3:112323961..112326448-chr3:112736769..112738621,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272761	TF binding region
ENSG00000091986	Chromatin interaction
ENSG00000240057	Chromatin interaction
ENSG00000163608	Chromatin interaction

Extended variants
information (count: 132 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:129)

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];0.92[EUR][1000 genomes]
rs13063173	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13064534	0.86[EUR][1000 genomes]
rs13065703	0.92[EUR][1000 genomes]
rs13070342	0.92[EUR][1000 genomes]
rs13071492	0.92[EUR][1000 genomes]
rs13078401	1.00[AFR][1000 genomes]
rs13079599	1.00[AFR][1000 genomes]
rs13080547	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13080749	0.92[EUR][1000 genomes]
rs13081201	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081265	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13081632	0.89[EUR][1000 genomes]
rs13086960	1.00[AFR][1000 genomes]
rs13088339	1.00[EUR][1000 genomes]
rs13088349	1.00[EUR][1000 genomes]
rs13088467	1.00[EUR][1000 genomes]
rs13094161	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13094649	0.92[EUR][1000 genomes]
rs13095000	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096943	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs16845067	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[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[EUR][1000 genomes]
rs16859758	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs16859775	0.83[ASN][1000 genomes]
rs16859779	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16859787	1.00[EUR][1000 genomes]
rs16859793	1.00[EUR][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	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705526	0.85[EUR][1000 genomes]
rs28364588	1.00[AFR][1000 genomes]
rs28364589	1.00[AFR][1000 genomes]
rs28365853	1.00[EUR][1000 genomes]
rs34080815	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs34139211	0.92[EUR][1000 genomes]
rs34248586	0.92[EUR][1000 genomes]
rs34284082	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34596334	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34597203	0.92[EUR][1000 genomes]
rs34645913	0.92[EUR][1000 genomes]
rs34829517	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34889961	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs34949685	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34962178	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35107041	0.82[EUR][1000 genomes]
rs35240469	0.92[EUR][1000 genomes]
rs35255669	1.00[EUR][1000 genomes]
rs35263368	1.00[AFR][1000 genomes]
rs35349986	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35512450	0.92[EUR][1000 genomes]
rs35526995	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs35529363	1.00[EUR][1000 genomes]
rs35692417	1.00[EUR][1000 genomes]
rs35709173	1.00[EUR][1000 genomes]
rs35725070	0.92[EUR][1000 genomes]
rs35748518	0.92[EUR][1000 genomes]
rs35803911	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35840933	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35931975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36025914	1.00[EUR][1000 genomes]
rs36031379	0.83[EUR][1000 genomes]
rs36045008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36061184	1.00[EUR][1000 genomes]
rs36146261	1.00[EUR][1000 genomes]
rs36153507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736269	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3736270	0.92[EUR][1000 genomes]
rs3736271	0.92[EUR][1000 genomes]
rs3773698	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3773701	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3773704	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3773706	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3773710	1.00[EUR][1000 genomes]
rs3821684	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55742760	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56662636	0.92[EUR][1000 genomes]
rs56856838	0.92[EUR][1000 genomes]
rs56952692	1.00[AFR][1000 genomes]
rs56970524	1.00[EUR][1000 genomes]
rs57224143	1.00[AFR][1000 genomes]
rs57346109	0.92[EUR][1000 genomes]
rs58657519	1.00[AFR][1000 genomes]
rs58891772	0.92[EUR][1000 genomes]
rs59191788	1.00[AFR][1000 genomes]
rs59279185	0.92[EUR][1000 genomes]
rs59650289	1.00[AFR][1000 genomes]
rs59858117	0.92[EUR][1000 genomes]
rs60321074	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60340975	1.00[AFR][1000 genomes]
rs60646325	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60733172	1.00[AFR][1000 genomes]
rs66486470	0.92[EUR][1000 genomes]
rs66546764	1.00[AFR][1000 genomes]
rs66698345	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66791711	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66910014	0.92[EUR][1000 genomes]
rs67021100	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs67204151	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67513863	0.96[EUR][1000 genomes]
rs67940544	1.00[EUR][1000 genomes]
rs67944354	0.92[EUR][1000 genomes]
rs71317505	0.85[EUR][1000 genomes]
rs71317506	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs71317507	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs71317508	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs71317510	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724125	1.00[EUR][1000 genomes]
rs73229350	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs73229353	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs73229398	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs958935	1.00[EUR][1000 genomes]
rs963541	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112281800-112324200	Weak transcription	Spleen	Spleen
2	chr3:112281800-112325400	Weak transcription	Gastric	stomach
3	chr3:112282000-112330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:112282000-112330600	Weak transcription	Esophagus	oesophagus
5	chr3:112282400-112324200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:112282400-112340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:112298600-112325200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:112298800-112335200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:112300200-112331000	Weak transcription	Lung	lung
10	chr3:112300200-112334000	Weak transcription	Fetal Stomach	stomach
11	chr3:112302800-112324200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:112303800-112324200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr3:112305000-112324200	Weak transcription	Fetal Brain Male	brain
14	chr3:112305400-112330400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:112305600-112324200	Weak transcription	Fetal Kidney	kidney
16	chr3:112305800-112334800	Weak transcription	Aorta	Aorta
17	chr3:112307400-112329000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:112311600-112330600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:112311600-112331000	Weak transcription	Psoas Muscle	Psoas
20	chr3:112312400-112324200	Weak transcription	Ovary	ovary
21	chr3:112312400-112325200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:112312400-112326800	Weak transcription	Fetal Lung	lung
23	chr3:112312400-112331000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:112312600-112324200	Weak transcription	Brain Angular Gyrus	brain
25	chr3:112312600-112330400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:112312600-112346200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:112312600-112347200	Weak transcription	Fetal Intestine Large	intestine
28	chr3:112316000-112327400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr3:112316200-112342800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr3:112316400-112333600	Weak transcription	A549	lung
31	chr3:112316600-112337600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:112317000-112324200	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr3:112317600-112328600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr3:112318000-112341800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:112318200-112330600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:112318400-112324200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:112321400-112324200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:112321600-112324800	Genic enhancers	Osteobl	bone
39	chr3:112321800-112326400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:112322200-112337200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:112322600-112324400	Genic enhancers	Adipose Nuclei	Adipose
42	chr3:112322600-112325400	Genic enhancers	HSMM	muscle
43	chr3:112322800-112329400	Strong transcription	Colon Smooth Muscle	Colon
44	chr3:112323000-112324400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:112323000-112324400	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr3:112323000-112324600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:112323000-112324800	Genic enhancers	NHDF-Ad	bronchial
48	chr3:112323000-112325000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:112323000-112325200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:112323000-112325200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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