Variant report

Variant	rs67940544
Chromosome Location	chr3:112285956-112285957
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	chr3:112285735..112288489-chr3:112291503..112294225,2	K562	blood:
2	chr3:112279902..112282989-chr3:112283976..112287292,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138459	Chromatin interaction
ENSG00000144848	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10511317	0.85[EUR][1000 genomes]
rs11919639	0.82[EUR][1000 genomes]
rs11921669	0.82[EUR][1000 genomes]
rs13059364	0.92[EUR][1000 genomes]
rs13063173	0.92[EUR][1000 genomes]
rs13064534	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13065703	0.92[EUR][1000 genomes]
rs13070342	0.92[EUR][1000 genomes]
rs13071492	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13080547	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13080749	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13081201	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13081265	0.89[EUR][1000 genomes]
rs13081632	0.89[EUR][1000 genomes]
rs13088339	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13088349	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13088467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094161	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13094649	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13095000	1.00[EUR][1000 genomes]
rs13096943	0.89[EUR][1000 genomes]
rs16845067	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16859661	0.89[EUR][1000 genomes]
rs16859674	0.81[EUR][1000 genomes]
rs16859727	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs16859758	0.92[EUR][1000 genomes]
rs16859775	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs16859779	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16859787	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16859793	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1994711	0.88[AMR][1000 genomes]
rs1994712	0.90[AMR][1000 genomes]
rs2220656	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2705526	0.85[EUR][1000 genomes]
rs28365853	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2942062	0.88[AMR][1000 genomes]
rs34080815	0.92[EUR][1000 genomes]
rs34139211	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs34248586	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs34284082	0.96[EUR][1000 genomes]
rs34541731	1.00[EUR][1000 genomes]
rs34596334	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34597203	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs34645913	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs34829517	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34889961	0.92[EUR][1000 genomes]
rs34949685	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34962178	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35107041	0.82[EUR][1000 genomes]
rs35240469	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs35255669	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35349986	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35512450	0.92[EUR][1000 genomes]
rs35526995	0.92[EUR][1000 genomes]
rs35529363	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35692417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35709173	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35725070	0.92[EUR][1000 genomes]
rs35748518	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs35803911	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35840933	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35931975	1.00[EUR][1000 genomes]
rs36025914	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36031379	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs36045008	1.00[EUR][1000 genomes]
rs36061184	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36146261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36153507	1.00[EUR][1000 genomes]
rs3736269	0.92[EUR][1000 genomes]
rs3736270	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3736271	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3773698	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3773701	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3773704	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3773706	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3773710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821684	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55742760	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56662636	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs56856838	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs56970524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57346109	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs58891772	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs59279185	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs59305071	0.94[AFR][1000 genomes]
rs59858117	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs60321074	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60646325	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66486470	0.92[EUR][1000 genomes]
rs66698345	0.96[EUR][1000 genomes]
rs66791711	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66910014	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs67021100	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67204151	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67513863	0.96[EUR][1000 genomes]
rs67944354	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs71317505	0.85[EUR][1000 genomes]
rs71317506	0.89[EUR][1000 genomes]
rs71317507	0.92[EUR][1000 genomes]
rs71317508	0.92[EUR][1000 genomes]
rs71317510	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs724125	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73229350	0.92[EUR][1000 genomes]
rs73229353	0.92[EUR][1000 genomes]
rs73229398	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs958935	1.00[AFR][1000 genomes];1.00[EUR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs67940544	SLC35A5	cis	Nerve Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112281800-112286200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:112281800-112287000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:112281800-112289800	Weak transcription	HSMMtube	muscle
4	chr3:112281800-112290400	Weak transcription	Lung	lung
5	chr3:112281800-112291400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:112281800-112299400	Weak transcription	Left Ventricle	heart
7	chr3:112281800-112301600	Weak transcription	HepG2	liver
8	chr3:112281800-112312000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:112281800-112315400	Weak transcription	Pancreas	Pancrea
10	chr3:112281800-112324200	Weak transcription	Spleen	Spleen
11	chr3:112281800-112325400	Weak transcription	Gastric	stomach
12	chr3:112282000-112287200	Weak transcription	Aorta	Aorta
13	chr3:112282000-112288200	Weak transcription	Ovary	ovary
14	chr3:112282000-112289600	Weak transcription	Colonic Mucosa	Colon
15	chr3:112282000-112312200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:112282000-112330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:112282000-112330600	Weak transcription	Esophagus	oesophagus
18	chr3:112282200-112286400	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:112282200-112287200	Weak transcription	HSMM	muscle
20	chr3:112282200-112303400	Weak transcription	Psoas Muscle	Psoas
21	chr3:112282400-112286000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:112282400-112286000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:112282400-112287000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:112282400-112287400	Weak transcription	NH-A	brain
25	chr3:112282400-112287400	Weak transcription	Osteobl	bone
26	chr3:112282400-112288200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:112282400-112289000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:112282400-112289200	Weak transcription	Brain Substantia Nigra	brain
29	chr3:112282400-112289800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:112282400-112290400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:112282400-112290400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:112282400-112291200	Weak transcription	NHLF	lung
33	chr3:112282400-112291800	Weak transcription	Fetal Kidney	kidney
34	chr3:112282400-112299400	Weak transcription	Fetal Stomach	stomach
35	chr3:112282400-112301600	Weak transcription	Hela-S3	cervix
36	chr3:112282400-112304400	Weak transcription	Fetal Heart	heart
37	chr3:112282400-112306600	Weak transcription	Right Ventricle	heart
38	chr3:112282400-112307200	Weak transcription	Small Intestine	intestine
39	chr3:112282400-112312400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:112282400-112316800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:112282400-112322800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:112282400-112324200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:112282400-112340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:112282600-112286400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr3:112282600-112287000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:112282600-112287000	Weak transcription	HMEC	breast
47	chr3:112282600-112287200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:112282600-112287400	Weak transcription	HUVEC	blood vessel
49	chr3:112282600-112287600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:112282600-112288200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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