Variant report

Variant	rs56662636
Chromosome Location	chr3:112246210-112246211
allele	C/T
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	TCF3	chr3:112245993-112246233	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATG3-1	chr3:112244395-112246989	NONHSAT091182

Variant related genes	Relation type
OR7E100P	TF binding region

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10511317	0.92[EUR][1000 genomes]
rs11919639	0.89[EUR][1000 genomes]
rs11921669	0.89[EUR][1000 genomes]
rs13059364	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13063173	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13064534	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065703	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070342	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13071492	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13080547	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13080749	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13081201	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13081265	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13081632	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13088339	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13088349	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13088467	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13092057	0.85[EUR][1000 genomes]
rs13094161	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13094649	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095000	0.92[EUR][1000 genomes]
rs13096943	0.96[EUR][1000 genomes]
rs16845067	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16859661	0.96[EUR][1000 genomes]
rs16859674	0.89[EUR][1000 genomes]
rs16859727	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859758	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859775	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16859779	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16859787	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16859793	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2220656	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2705526	0.92[EUR][1000 genomes]
rs28365853	0.92[EUR][1000 genomes]
rs34080815	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34139211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34248586	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34284082	0.89[EUR][1000 genomes]
rs34541731	0.92[EUR][1000 genomes]
rs34596334	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34597203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34645913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34829517	0.92[EUR][1000 genomes]
rs34889961	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34949685	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34962178	0.92[EUR][1000 genomes]
rs35107041	0.89[EUR][1000 genomes]
rs35240469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35255669	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35349986	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35512450	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35526995	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35529363	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35692417	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs35709173	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35725070	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35748518	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35803911	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35840933	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs35931975	0.92[EUR][1000 genomes]
rs36025914	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36031379	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36045008	0.92[EUR][1000 genomes]
rs36061184	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36146261	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs36153507	0.92[EUR][1000 genomes]
rs3736269	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736270	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736271	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773698	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3773701	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3773704	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3773706	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3773710	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3821684	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55742760	0.92[EUR][1000 genomes]
rs56856838	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56970524	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs57346109	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58891772	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59279185	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59305071	0.98[AFR][1000 genomes]
rs59858117	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60321074	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs60646325	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66486470	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66698345	0.89[EUR][1000 genomes]
rs66791711	0.92[EUR][1000 genomes]
rs66910014	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67021100	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67204151	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67513863	0.89[EUR][1000 genomes]
rs67940544	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs67944354	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71317505	0.92[EUR][1000 genomes]
rs71317506	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71317507	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71317508	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71317510	0.92[EUR][1000 genomes]
rs724125	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73229350	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73229353	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73229398	0.92[EUR][1000 genomes]
rs958935	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv591300	chr3:112144026-112270857	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	nsv965197	chr3:112238965-112250194	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56662636	SLC35A5	cis	Nerve Tibial	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112227400-112269800	Weak transcription	Small Intestine	intestine
2	chr3:112231600-112246800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:112234000-112247600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:112234200-112272000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:112237000-112247000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:112237200-112247400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:112237200-112254200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr3:112238200-112247000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr3:112238200-112247400	Weak transcription	GM12878-XiMat	blood
10	chr3:112238600-112249200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:112239600-112272200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:112239800-112247200	Weak transcription	Lung	lung
13	chr3:112239800-112247400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:112239800-112247800	Weak transcription	Aorta	Aorta
15	chr3:112239800-112247800	Weak transcription	Esophagus	oesophagus
16	chr3:112240600-112246600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:112241000-112246400	Weak transcription	Fetal Muscle Leg	muscle
18	chr3:112241000-112251600	Weak transcription	HUVEC	blood vessel
19	chr3:112241600-112259400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr3:112242000-112247400	Weak transcription	Spleen	Spleen
21	chr3:112242000-112247800	Weak transcription	Gastric	stomach
22	chr3:112242000-112248400	Weak transcription	NHDF-Ad	bronchial
23	chr3:112242200-112247000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:112242200-112247400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:112242200-112247600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:112242200-112248000	Weak transcription	Fetal Intestine Small	intestine
27	chr3:112242200-112252200	Weak transcription	NHLF	lung
28	chr3:112242400-112246800	Weak transcription	Fetal Thymus	thymus
29	chr3:112242400-112247800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:112242400-112247800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:112242400-112249800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:112242600-112263800	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr3:112243000-112271600	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr3:112243400-112247400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr3:112243600-112247200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:112243800-112247000	Weak transcription	Ovary	ovary
37	chr3:112244000-112246600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:112244000-112246800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr3:112244000-112247000	Weak transcription	Fetal Stomach	stomach
40	chr3:112244000-112247400	Weak transcription	Brain Anterior Caudate	brain
41	chr3:112244000-112259800	Weak transcription	Pancreas	Pancrea
42	chr3:112244200-112246800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr3:112244200-112247400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr3:112244200-112247600	Weak transcription	Fetal Lung	lung
45	chr3:112244200-112251200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:112244400-112247000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:112244400-112247000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr3:112244400-112247000	Weak transcription	Right Ventricle	heart
49	chr3:112244400-112247000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr3:112244400-112247400	Weak transcription	Colonic Mucosa	Colon

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